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PDBsum entry 1udh
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Contents |
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* Residue conservation analysis
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Nature
373:487-493
(1995)
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PubMed id:
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The structural basis of specific base-excision repair by uracil-DNA glycosylase.
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R.Savva,
K.McAuley-Hecht,
T.Brown,
L.Pearl.
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ABSTRACT
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The 1.75-A crystal structure of the uracil-DNA glycosylase from herpes simplex
virus type-1 reveals a new fold, distantly related to dinucleotide-binding
proteins. Complexes with a trideoxynucleotide, and with uracil, define the
DNA-binding site and allow a detailed understanding of the exquisitely specific
recognition of uracil in DNA. The overall structure suggests binding models for
elongated single- and double-stranded DNA substrates. Conserved residues close
to the uracil-binding site suggest a catalytic mechanism for hydrolytic base
excision.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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D.O.Zharkov,
G.V.Mechetin,
and
G.A.Nevinsky
(2010).
Uracil-DNA glycosylase: Structural, thermodynamic and kinetic aspects of lesion search and recognition.
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Mutat Res,
685,
11-20.
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H.A.Cole,
J.M.Tabor-Godwin,
and
J.J.Hayes
(2010).
Uracil DNA glycosylase activity on nucleosomal DNA depends on rotational orientation of targets.
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J Biol Chem,
285,
2876-2885.
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G.L.Randall,
L.Zechiedrich,
and
B.M.Pettitt
(2009).
In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form.
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Nucleic Acids Res,
37,
5568-5577.
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B.Mercorelli,
E.Sinigalia,
A.Loregian,
and
G.Palù
(2008).
Human cytomegalovirus DNA replication: antiviral targets and drugs.
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Rev Med Virol,
18,
177-210.
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G.A.Kim,
M.S.Lee,
Y.Sun,
B.D.Lee,
J.I.Lee,
J.H.Lee,
and
S.T.Kwon
(2008).
Characterization of cold-active uracil-DNA glycosylase from Bacillus sp. HJ171 and its use for contamination control in PCR.
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Appl Microbiol Biotechnol,
80,
785-794.
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I.Hudáky,
and
A.Perczel
(2008).
Prolylproline unit in model peptides and in fragments from databases.
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Proteins,
70,
1389-1407.
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M.Olufsen,
A.O.Smalås,
and
B.O.Brandsdal
(2008).
Electrostatic interactions play an essential role in DNA repair and cold-adaptation of Uracil DNA glycosylase.
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J Mol Model,
14,
201-213.
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M.Olufsen,
E.Papaleo,
A.O.Smalås,
and
B.O.Brandsdal
(2008).
Ion pairs and their role in modulating stability of cold- and warm-active uracil DNA glycosylase.
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Proteins,
71,
1219-1230.
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P.Liu,
J.A.Theruvathu,
A.Darwanto,
V.V.Lao,
T.Pascal,
W.Goddard,
and
L.C.Sowers
(2008).
Mechanisms of base selection by the Escherichia coli mispaired uracil glycosylase.
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J Biol Chem,
283,
8829-8836.
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P.S.Kaushal,
R.K.Talawar,
P.D.Krishna,
U.Varshney,
and
M.Vijayan
(2008).
Unique features of the structure and interactions of mycobacterial uracil-DNA glycosylase: structure of a complex of the Mycobacterium tuberculosis enzyme in comparison with those from other sources.
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Acta Crystallogr D Biol Crystallogr,
64,
551-560.
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PDB code:
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R.D.Shereda,
A.G.Kozlov,
T.M.Lohman,
M.M.Cox,
and
J.L.Keck
(2008).
SSB as an organizer/mobilizer of genome maintenance complexes.
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Crit Rev Biochem Mol Biol,
43,
289-318.
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C.C.Lu,
H.T.Huang,
J.T.Wang,
G.Slupphaug,
T.K.Li,
M.C.Wu,
Y.C.Chen,
C.P.Lee,
and
M.R.Chen
(2007).
Characterization of the uracil-DNA glycosylase activity of Epstein-Barr virus BKRF3 and its role in lytic viral DNA replication.
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J Virol,
81,
1195-1208.
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H.Gao,
J.Huang,
F.Barany,
and
W.Cao
(2007).
Switching base preferences of mismatch cleavage in endonuclease V: an improved method for scanning point mutations.
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Nucleic Acids Res,
35,
e2.
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N.Schormann,
A.Grigorian,
A.Samal,
R.Krishnan,
L.DeLucas,
and
D.Chattopadhyay
(2007).
Crystal structure of vaccinia virus uracil-DNA glycosylase reveals dimeric assembly.
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BMC Struct Biol,
7,
45.
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PDB codes:
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S.R.Bellamy,
K.Krusong,
and
G.S.Baldwin
(2007).
A rapid reaction analysis of uracil DNA glycosylase indicates an active mechanism of base flipping.
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Nucleic Acids Res,
35,
1478-1487.
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C.Cao,
Y.L.Jiang,
D.J.Krosky,
and
J.T.Stivers
(2006).
The catalytic power of uracil DNA glycosylase in the opening of thymine base pairs.
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J Am Chem Soc,
128,
13034-13035.
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J.Georg,
L.Schomacher,
J.P.Chong,
A.I.Majerník,
M.Raabe,
H.Urlaub,
S.Müller,
E.Ciirdaeva,
W.Kramer,
and
H.J.Fritz
(2006).
The Methanothermobacter thermautotrophicus ExoIII homologue Mth212 is a DNA uridine endonuclease.
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Nucleic Acids Res,
34,
5325-5336.
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K.Krusong,
E.P.Carpenter,
S.R.Bellamy,
R.Savva,
and
G.S.Baldwin
(2006).
A comparative study of uracil-DNA glycosylases from human and herpes simplex virus type 1.
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J Biol Chem,
281,
4983-4992.
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PDB codes:
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P.Singh,
R.K.Talawar,
P.D.Krishna,
U.Varshney,
and
M.Vijayan
(2006).
Overexpression, purification, crystallization and preliminary X-ray analysis of uracil N-glycosylase from Mycobacterium tuberculosis in complex with a proteinaceous inhibitor.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
62,
1231-1234.
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I.Leiros,
E.Moe,
A.O.Smalås,
and
S.McSweeney
(2005).
Structure of the uracil-DNA N-glycosylase (UNG) from Deinococcus radiodurans.
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Acta Crystallogr D Biol Crystallogr,
61,
1049-1056.
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PDB code:
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M.Olufsen,
A.O.Smalås,
E.Moe,
and
B.O.Brandsdal
(2005).
Increased flexibility as a strategy for cold adaptation: a comparative molecular dynamics study of cold- and warm-active uracil DNA glycosylase.
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J Biol Chem,
280,
18042-18048.
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R.Steinacher,
and
P.Schär
(2005).
Functionality of human thymine DNA glycosylase requires SUMO-regulated changes in protein conformation.
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Curr Biol,
15,
616-623.
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Y.L.Jiang,
D.J.Krosky,
L.Seiple,
and
J.T.Stivers
(2005).
Uracil-directed ligand tethering: an efficient strategy for uracil DNA glycosylase (UNG) inhibitor development.
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J Am Chem Soc,
127,
17412-17420.
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J.C.Fromme,
A.Banerjee,
and
G.L.Verdine
(2004).
DNA glycosylase recognition and catalysis.
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Curr Opin Struct Biol,
14,
43-49.
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J.M.Gulbis,
S.L.Kazmirski,
J.Finkelstein,
Z.Kelman,
M.O'Donnell,
and
J.Kuriyan
(2004).
Crystal structure of the chi:psi sub-assembly of the Escherichia coli DNA polymerase clamp-loader complex.
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Eur J Biochem,
271,
439-449.
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PDB code:
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M.Matsubara,
T.Tanaka,
H.Terato,
E.Ohmae,
S.Izumi,
K.Katayanagi,
and
H.Ide
(2004).
Mutational analysis of the damage-recognition and catalytic mechanism of human SMUG1 DNA glycosylase.
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Nucleic Acids Res,
32,
5291-5302.
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T.J.Su,
B.A.Connolly,
C.Darlington,
R.Mallin,
and
D.T.Dryden
(2004).
Unusual 2-aminopurine fluorescence from a complex of DNA and the EcoKI methyltransferase.
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Nucleic Acids Res,
32,
2223-2230.
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T.Torizawa,
T.Ueda,
S.Kuramitsu,
K.Hitomi,
T.Todo,
S.Iwai,
K.Morikawa,
and
I.Shimada
(2004).
Investigation of the cyclobutane pyrimidine dimer (CPD) photolyase DNA recognition mechanism by NMR analyses.
|
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J Biol Chem,
279,
32950-32956.
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F.S.De Silva,
and
B.Moss
(2003).
Vaccinia virus uracil DNA glycosylase has an essential role in DNA synthesis that is independent of its glycosylase activity: catalytic site mutations reduce virulence but not virus replication in cultured cells.
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J Virol,
77,
159-166.
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I.Leiros,
E.Moe,
O.Lanes,
A.O.Smalås,
and
N.P.Willassen
(2003).
The structure of uracil-DNA glycosylase from Atlantic cod (Gadus morhua) reveals cold-adaptation features.
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Acta Crystallogr D Biol Crystallogr,
59,
1357-1365.
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PDB code:
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J.E.Wibley,
T.R.Waters,
K.Haushalter,
G.L.Verdine,
and
L.H.Pearl
(2003).
Structure and specificity of the vertebrate anti-mutator uracil-DNA glycosylase SMUG1.
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Mol Cell,
11,
1647-1659.
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PDB codes:
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J.H.Chung,
E.K.Im,
H.Y.Park,
J.H.Kwon,
S.Lee,
J.Oh,
K.C.Hwang,
J.H.Lee,
and
Y.Jang
(2003).
A novel uracil-DNA glycosylase family related to the helix-hairpin-helix DNA glycosylase superfamily.
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Nucleic Acids Res,
31,
2045-2055.
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N.Acharya,
R.K.Talawar,
K.Saikrishnan,
M.Vijayan,
and
U.Varshney
(2003).
Substitutions at tyrosine 66 of Escherichia coli uracil DNA glycosylase lead to characterization of an efficient enzyme that is recalcitrant to product inhibition.
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Nucleic Acids Res,
31,
7216-7226.
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R.J.O'Neill,
O.V.Vorob'eva,
H.Shahbakhti,
E.Zmuda,
A.S.Bhagwat,
and
G.S.Baldwin
(2003).
Mismatch uracil glycosylase from Escherichia coli: a general mismatch or a specific DNA glycosylase?
|
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J Biol Chem,
278,
20526-20532.
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A.A.Ishchenko,
N.L.Vasilenko,
O.I.Sinitsina,
V.I.Yamkovoy,
O.S.Fedorova,
K.T.Douglas,
and
G.A.Nevinsky
(2002).
Thermodynamic, kinetic, and structural basis for recognition and repair of 8-oxoguanine in DNA by Fpg protein from Escherichia coli.
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Biochemistry,
41,
7540-7548.
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A.C.Vallur,
J.A.Feller,
C.W.Abner,
R.K.Tran,
and
L.B.Bloom
(2002).
Effects of hydrogen bonding within a damaged base pair on the activity of wild type and DNA-intercalating mutants of human alkyladenine DNA glycosylase.
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J Biol Chem,
277,
31673-31678.
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D.O.Zharkov,
and
A.P.Grollman
(2002).
Combining structural and bioinformatics methods for the analysis of functionally important residues in DNA glycosylases.
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Free Radic Biol Med,
32,
1254-1263.
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I.Wong,
A.J.Lundquist,
A.S.Bernards,
and
D.W.Mosbaugh
(2002).
Presteady-state analysis of a single catalytic turnover by Escherichia coli uracil-DNA glycosylase reveals a "pinch-pull-push" mechanism.
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J Biol Chem,
277,
19424-19432.
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K.S.Yan,
and
M.M.Zhou
(2002).
TAGging the target for damage control.
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Nat Struct Biol,
9,
638-640.
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K.Saikrishnan,
M.Bidya Sagar,
R.Ravishankar,
S.Roy,
K.Purnapatre,
P.Handa,
U.Varshney,
and
M.Vijayan
(2002).
Domain closure and action of uracil DNA glycosylase (UDG): structures of new crystal forms containing the Escherichia coli enzyme and a comparative study of the known structures involving UDG.
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Acta Crystallogr D Biol Crystallogr,
58,
1269-1276.
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PDB codes:
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M.A.Kurinovich,
and
J.K.Lee
(2002).
The acidity of uracil and uracil analogs in the gas phase: four surprisingly acidic sites and biological implications.
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J Am Soc Mass Spectrom,
13,
985-995.
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P.Handa,
N.Acharya,
and
U.Varshney
(2002).
Effects of mutations at tyrosine 66 and asparagine 123 in the active site pocket of Escherichia coli uracil DNA glycosylase on uracil excision from synthetic DNA oligomers: evidence for the occurrence of long-range interactions between the enzyme and substrate.
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Nucleic Acids Res,
30,
3086-3095.
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Y.W.Kow
(2002).
Repair of deaminated bases in DNA.
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Free Radic Biol Med,
33,
886-893.
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Z.Morávek,
S.Neidle,
and
B.Schneider
(2002).
Protein and drug interactions in the minor groove of DNA.
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Nucleic Acids Res,
30,
1182-1191.
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C.J.Norbury,
and
I.D.Hickson
(2001).
Cellular responses to DNA damage.
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Annu Rev Pharmacol Toxicol,
41,
367-401.
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I.Leiros,
O.Lanes,
O.Sundheim,
R.Helland,
A.O.Smalås,
and
N.P.Willassen
(2001).
Crystallization and preliminary X-ray diffraction analysis of a cold-adapted uracil-DNA glycosylase from Atlantic cod (Gadus morhua).
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Acta Crystallogr D Biol Crystallogr,
57,
1706-1708.
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M.E.Fárez-Vidal,
C.Gallego,
L.M.Ruiz-Pérez,
and
D.González-Pacanowska
(2001).
Characterization of uracil-DNA glycosylase activity from Trypanosoma cruzi and its stimulation by AP endonuclease.
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Nucleic Acids Res,
29,
1549-1555.
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N.H.Chmiel,
M.P.Golinelli,
A.W.Francis,
and
S.S.David
(2001).
Efficient recognition of substrates and substrate analogs by the adenine glycosylase MutY requires the C-terminal domain.
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Nucleic Acids Res,
29,
553-564.
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O.D.Schärer,
and
J.Jiricny
(2001).
Recent progress in the biology, chemistry and structural biology of DNA glycosylases.
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Bioessays,
23,
270-281.
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T.D.Schneider
(2001).
Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation.
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| |
Nucleic Acids Res,
29,
4881-4891.
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J.Dong,
A.C.Drohat,
J.T.Stivers,
K.W.Pankiewicz,
and
P.R.Carey
(2000).
Raman spectroscopy of uracil DNA glycosylase-DNA complexes: insights into DNA damage recognition and catalysis.
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| |
Biochemistry,
39,
13241-13250.
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L.Aravind,
and
E.V.Koonin
(2000).
The alpha/beta fold uracil DNA glycosylases: a common origin with diverse fates.
|
| |
Genome Biol,
1,
RESEARCH0007.
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M.Saparbaev,
J.C.Mani,
and
J.Laval
(2000).
Interactions of the human, rat, Saccharomyces cerevisiae and Escherichia coli 3-methyladenine-DNA glycosylases with DNA containing dIMP residues.
|
| |
Nucleic Acids Res,
28,
1332-1339.
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R.M.Werner,
Y.L.Jiang,
R.G.Gordley,
G.J.Jagadeesh,
J.E.Ladner,
G.Xiao,
M.Tordova,
G.L.Gilliland,
and
J.T.Stivers
(2000).
Stressing-out DNA? The contribution of serine-phosphodiester interactions in catalysis by uracil DNA glycosylase.
|
| |
Biochemistry,
39,
12585-12594.
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PDB code:
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R.Roy,
T.Biswas,
J.C.Lee,
and
S.Mitra
(2000).
Mutation of a unique aspartate residue abolishes the catalytic activity but not substrate binding of the mouse N-methylpurine-DNA glycosylase (MPG).
|
| |
J Biol Chem,
275,
4278-4282.
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S.Datta,
M.M.Prabu,
M.B.Vaze,
N.Ganesh,
N.R.Chandra,
K.Muniyappa,
and
M.Vijayan
(2000).
Crystal structures of Mycobacterium tuberculosis RecA and its complex with ADP-AlF(4): implications for decreased ATPase activity and molecular aggregation.
|
| |
Nucleic Acids Res,
28,
4964-4973.
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PDB codes:
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S.S.Parikh,
G.Walcher,
G.D.Jones,
G.Slupphaug,
H.E.Krokan,
G.M.Blackburn,
and
J.A.Tainer
(2000).
Uracil-DNA glycosylase-DNA substrate and product structures: conformational strain promotes catalytic efficiency by coupled stereoelectronic effects.
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| |
Proc Natl Acad Sci U S A,
97,
5083-5088.
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PDB codes:
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A.K.McCullough,
M.L.Dodson,
and
R.S.Lloyd
(1999).
Initiation of base excision repair: glycosylase mechanisms and structures.
|
| |
Annu Rev Biochem,
68,
255-285.
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B.W.Allan,
R.Garcia,
K.Maegley,
J.Mort,
D.Wong,
W.Lindstrom,
J.M.Beechem,
and
N.O.Reich
(1999).
DNA bending by EcoRI DNA methyltransferase accelerates base flipping but compromises specificity.
|
| |
J Biol Chem,
274,
19269-19275.
|
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C.D.Mol,
S.S.Parikh,
C.D.Putnam,
T.P.Lo,
and
J.A.Tainer
(1999).
DNA repair mechanisms for the recognition and removal of damaged DNA bases.
|
| |
Annu Rev Biophys Biomol Struct,
28,
101-128.
|
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D.M.van Aalten,
D.A.Erlanson,
G.L.Verdine,
and
L.Joshua-Tor
(1999).
A structural snapshot of base-pair opening in DNA.
|
| |
Proc Natl Acad Sci U S A,
96,
11809-11814.
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PDB code:
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G.Xiao,
M.Tordova,
J.Jagadeesh,
A.C.Drohat,
J.T.Stivers,
and
G.L.Gilliland
(1999).
Crystal structure of Escherichia coli uracil DNA glycosylase and its complexes with uracil and glycerol: structure and glycosylase mechanism revisited.
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Proteins,
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PDB codes:
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|
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|
|
J.T.Stivers,
K.W.Pankiewicz,
and
K.A.Watanabe
(1999).
Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase.
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Biochemistry,
38,
952-963.
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K.A.Haushalter,
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M.W.Kirschner,
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(1999).
Identification of a new uracil-DNA glycosylase family by expression cloning using synthetic inhibitors.
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Curr Biol,
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M.A.Greagg,
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A read-ahead function in archaeal DNA polymerases detects promutagenic template-strand uracil.
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Proc Natl Acad Sci U S A,
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Mutation of an active site residue in Escherichia coli uracil-DNA glycosylase: effect on DNA binding, uracil inhibition and catalysis.
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Biochemistry,
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N.Luo,
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Specificity and catalysis of uracil DNA glycosylase. A molecular dynamics study of reactant and product complexes with DNA.
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Biochemistry,
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Envisioning the molecular choreography of DNA base excision repair.
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Curr Opin Struct Biol,
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(1999).
Crystal structure of a thwarted mismatch glycosylase DNA repair complex.
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EMBO J,
18,
6599-6609.
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PDB code:
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Y.X.Wang,
N.Neamati,
J.Jacob,
I.Palmer,
S.J.Stahl,
J.D.Kaufman,
P.L.Huang,
P.L.Huang,
H.E.Winslow,
Y.Pommier,
P.T.Wingfield,
S.Lee-Huang,
A.Bax,
and
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(1999).
Solution structure of anti-HIV-1 and anti-tumor protein MAP30: structural insights into its multiple functions.
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Cell,
99,
433-442.
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PDB code:
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C.Schmutte,
and
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(1998).
Involvement of DNA methylation in human carcinogenesis.
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Biol Chem,
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Protein-mediated base flipping.
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Curr Opin Biotechnol,
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Direct measurement of the substrate preference of uracil-DNA glycosylase.
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J Biol Chem,
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Trypanosomal nucleoside hydrolase. A novel mechanism from the structure with a transition-state inhibitor.
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Biochemistry,
37,
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PDB code:
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M.Saparbaev,
and
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(1998).
3,N4-ethenocytosine, a highly mutagenic adduct, is a primary substrate for Escherichia coli double-stranded uracil-DNA glycosylase and human mismatch-specific thymine-DNA glycosylase.
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Proc Natl Acad Sci U S A,
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(1998).
Structures of apurinic and apyrimidinic sites in duplex DNAs.
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J Biol Chem,
273,
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PDB codes:
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R.J.Roberts,
and
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(1998).
Base flipping.
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Annu Rev Biochem,
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Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA.
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EMBO J,
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PDB codes:
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T.E.Barrett,
R.Savva,
G.Panayotou,
T.Barlow,
T.Brown,
J.Jiricny,
and
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(1998).
Crystal structure of a G:T/U mismatch-specific DNA glycosylase: mismatch recognition by complementary-strand interactions.
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Cell,
92,
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PDB codes:
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T.R.Waters,
and
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(1998).
Kinetics of the action of thymine DNA glycosylase.
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J Biol Chem,
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Site-directed mutagenesis and characterization of uracil-DNA glycosylase inhibitor protein. Role of specific carboxylic amino acids in complex formation with Escherichia coli uracil-DNA glycosylase.
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J Biol Chem,
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The role of base flipping in damage recognition and catalysis by T4 endonuclease V.
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J Biol Chem,
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A.V.Efimov
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Structural trees for protein superfamilies.
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Proteins,
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From footprint to toeprint: a close-up of the DnaA box, the binding site for the bacterial initiator protein DnaA.
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Nucleic Acids Res,
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D.G.Vassylyev,
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DNA-repair enzymes.
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Curr Opin Struct Biol,
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Nick sensing by vaccinia virus DNA ligase requires a 5' phosphate at the nick and occupancy of the adenylate binding site on the enzyme.
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J Virol,
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L.E.Rabow,
and
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Mechanism of action of base release by Escherichia coli Fpg protein: role of lysine 155 in catalysis.
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Biochemistry,
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M.Yao,
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Further characterization of Escherichia coli endonuclease V. Mechanism of recognition for deoxyinosine, deoxyuridine, and base mismatches in DNA.
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J Biol Chem,
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Contrasting effects of single stranded DNA binding protein on the activity of uracil DNA glycosylase from Escherichia coli towards different DNA substrates.
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Nucleic Acids Res,
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Herpes simplex virus DNA replication.
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Annu Rev Biochem,
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(1997).
Cloning, overexpression, and biochemical characterization of the catalytic domain of MutY.
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Biochemistry,
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Mechanistic link between DNA methyltransferases and DNA repair enzymes by base flipping.
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Biopolymers,
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(1997).
DNA distortion and base flipping by the EcoRV DNA methyltransferase. A study using interference at dA and T bases and modified deoxynucleosides.
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J Biol Chem,
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The role of cysteine residues in the rearrangement of uridine to pseudouridine catalyzed by pseudouridine synthase I.
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J Biol Chem,
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A.B.Britt
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DNA DAMAGE AND REPAIR IN PLANTS.
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Annu Rev Plant Physiol Plant Mol Biol,
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Uracil-DNA glycosylase activities in hyperthermophilic micro-organisms.
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FEMS Microbiol Lett,
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B.Kavli,
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Excision of cytosine and thymine from DNA by mutants of human uracil-DNA glycosylase.
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EMBO J,
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(1996).
Targeted base stacking disruption by the EcoRI DNA methyltransferase.
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Biochemistry,
35,
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C.D.Mol,
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E.M.McIntosh,
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(1996).
Human dUTP pyrophosphatase: uracil recognition by a beta hairpin and active sites formed by three separate subunits.
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Structure,
4,
1077-1092.
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PDB codes:
|
|
|
|
|
|
|
|
D.G.Vassylyev,
and
K.Morikawa
(1996).
Precluding uracil from DNA.
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Structure,
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F.C.Christians,
and
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Novel human DNA alkyltransferases obtained by random substitution and genetic selection in bacteria.
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Proc Natl Acad Sci U S A,
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H.S.Subramanya,
A.J.Doherty,
S.R.Ashford,
and
D.B.Wigley
(1996).
Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7.
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Cell,
85,
607-615.
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PDB code:
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K.S.Ellison,
W.Peng,
and
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(1996).
Mutations in active-site residues of the uracil-DNA glycosylase encoded by vaccinia virus are incompatible with virus viability.
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J Virol,
70,
7965-7973.
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K.Scheffzek,
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L.Wiesmüller,
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Crystal structure of the complex of UMP/CMP kinase from Dictyostelium discoideum and the bisubstrate inhibitor P1-(5'-adenosyl) P5-(5'-uridyl) pentaphosphate (UP5A) and Mg2+ at 2.2 A: implications for water-mediated specificity.
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| |
Biochemistry,
35,
9716-9727.
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PDB codes:
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|
|
|
|
|
|
|
L.H.Pearl,
and
R.Savva
(1996).
The problem with pyrimidines.
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| |
Nat Struct Biol,
3,
485-487.
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M.Degano,
D.N.Gopaul,
G.Scapin,
V.L.Schramm,
and
J.C.Sacchettini
(1996).
Three-dimensional structure of the inosine-uridine nucleoside N-ribohydrolase from Crithidia fasciculata.
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| |
Biochemistry,
35,
5971-5981.
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PDB code:
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M.N.Prichard,
G.M.Duke,
and
E.S.Mocarski
(1996).
Human cytomegalovirus uracil DNA glycosylase is required for the normal temporal regulation of both DNA synthesis and viral replication.
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J Virol,
70,
3018-3025.
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O.N.Jensen,
S.Kulkarni,
J.V.Aldrich,
and
D.F.Barofsky
(1996).
Characterization of peptide-oligonucleotide heteroconjugates by mass spectrometry.
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Nucleic Acids Res,
24,
3866-3872.
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P.J.Day,
S.R.Ernst,
A.E.Frankel,
A.F.Monzingo,
J.M.Pascal,
M.C.Molina-Svinth,
and
J.D.Robertus
(1996).
Structure and activity of an active site substitution of ricin A chain.
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| |
Biochemistry,
35,
11098-11103.
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PDB codes:
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P.W.Laird,
and
R.Jaenisch
(1996).
The role of DNA methylation in cancer genetic and epigenetics.
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Annu Rev Genet,
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R.A.Garcia,
C.J.Bustamante,
and
N.O.Reich
(1996).
Sequence-specific recognition of cytosine C5 and adenine N6 DNA methyltransferases requires different deformations of DNA.
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Proc Natl Acad Sci U S A,
93,
7618-7622.
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R.J.Sanderson,
and
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(1996).
Identification of specific carboxyl groups on uracil-DNA glycosylase inhibitor protein that are required for activity.
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J Biol Chem,
271,
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R.Roy,
A.Kumar,
J.C.Lee,
and
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(1996).
The domains of mammalian base excision repair enzyme N-methylpurine-DNA glycosylase. Interaction, conformational change, and role in DNA binding and damage recognition.
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J Biol Chem,
271,
23690-23697.
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R.S.Lasken,
D.M.Schuster,
and
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(1996).
Archaebacterial DNA polymerases tightly bind uracil-containing DNA.
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J Biol Chem,
271,
17692-17696.
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Sibghat-Ullah,
P.Gallinari,
Y.Z.Xu,
M.F.Goodman,
L.B.Bloom,
J.Jiricny,
and
R.S.Day
(1996).
Base analog and neighboring base effects on substrate specificity of recombinant human G:T mismatch-specific thymine DNA-glycosylase.
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Biochemistry,
35,
12926-12932.
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X.Cheng,
and
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(1996).
Finding a basis for flipping bases.
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Structure,
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A.Sancar
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Excision repair in mammalian cells.
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J Biol Chem,
270,
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Enzyme structures. DNA repair flips out.
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Curr Biol,
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B.Sun,
K.A.Latham,
M.L.Dodson,
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(1995).
Studies on the catalytic mechanism of five DNA glycosylases. Probing for enzyme-DNA imino intermediates.
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J Biol Chem,
270,
19501-19508.
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C.D.Mol,
A.S.Arvai,
R.J.Sanderson,
G.Slupphaug,
B.Kavli,
H.E.Krokan,
D.W.Mosbaugh,
and
J.A.Tainer
(1995).
Crystal structure of human uracil-DNA glycosylase in complex with a protein inhibitor: protein mimicry of DNA.
|
| |
Cell,
82,
701-708.
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PDB code:
|
|
|
|
|
|
|
|
C.R.Allerson,
and
G.L.Verdine
(1995).
Synthesis and biochemical evaluation of RNA containing an intrahelical disulfide crosslink.
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Chem Biol,
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667-675.
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D.G.Vassylyev,
T.Kashiwagi,
Y.Mikami,
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S.Iwai,
E.Ohtsuka,
and
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(1995).
Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition.
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| |
Cell,
83,
773-782.
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PDB code:
|
|
|
|
|
|
|
|
D.S.Thaler,
G.Tombline,
and
K.Zahn
(1995).
Short-patch reverse transcription in Escherichia coli.
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Genetics,
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L.Eide,
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The base excision repair pathway.
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Trends Biochem Sci,
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Refined solution structure of a DNA heteroduplex containing an aldehydic abasic site.
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J Biol Chem,
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J.E.Cleaver,
and
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If the shoe fits": clues on structural recognition of DNA damage.
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Cell,
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L.H.Pearl,
and
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DNA repair in three dimensions.
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Trends Biochem Sci,
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On base flipping.
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Cell,
82,
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R.Savva,
and
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(1995).
Nucleotide mimicry in the crystal structure of the uracil-DNA glycosylase-uracil glycosylase inhibitor protein complex.
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| |
Nat Struct Biol,
2,
752-757.
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PDB code:
|
|
|
|
|
|
|
|
R.Savva,
and
L.H.Pearl
(1995).
Cloning and expression of the uracil-DNA glycosylase inhibitor (UGI) from bacteriophage PBS-1 and crystallization of a uracil-DNA glycosylase-UGI complex.
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Proteins,
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S.Klimasauskas,
and
R.J.Roberts
(1995).
M.HhaI binds tightly to substrates containing mismatches at the target base.
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Nucleic Acids Res,
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T.Ellenberger
(1995).
Pocketing the difference: structures of uracil excision repair proteins.
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Chem Biol,
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
|
|
Links
