 |
PDBsum entry 1flz
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
PDB id:
|
|
|
|
| Name: |
|
Hydrolase
|
|
|
Title:
|
|
Uracil DNA glycosylase with uaap
|
|
Structure:
|
|
Uracil-DNA glycosylase. Chain: a. Synonym: udg. Engineered: yes. Mutation: yes
|
|
Source:
|
|
Escherichia coli. Organism_taxid: 37762. Strain: b. Expressed in: escherichia coli. Expression_system_taxid: 562
|
|
Resolution:
|
|
|
|
Authors:
|
|
R.M.Werner,Y.L.Jiang,R.G.Gordley,G.J.Jagadeesh,J.E.Ladner,G.Xiao, M.Tordova,G.L.Gilliland,J.T.Stivers
|
Key ref:
|
|
R.M.Werner
et al.
(2000).
Stressing-out DNA? The contribution of serine-phosphodiester interactions in catalysis by uracil DNA glycosylase.
Biochemistry,
39,
12585-12594.
PubMed id:
DOI:
|
|
|
Date:
|
|
|
15-Aug-00
|
Release date:
|
17-Jan-01
|
|
|
|
|
|
|
PROCHECK
|
|
|
|
|
|
Headers
|
|
|
|
References
|
|
|
|
|
|
|
|
P12295
(UNG_ECOLI) -
Uracil-DNA glycosylase from Escherichia coli (strain K12)
|
|
|
|
Seq:
Struc:
|
|
|
|
229 a.a.
228 a.a.*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Key: |
 |
PfamA domain |
|
|
 |
Secondary structure |
|
 |
CATH domain |
|
|
*
PDB and UniProt seqs differ
at 2 residue positions (black
crosses)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
Biochemistry
39:12585-12594
(2000)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Stressing-out DNA? The contribution of serine-phosphodiester interactions in catalysis by uracil DNA glycosylase.
|
|
R.M.Werner,
Y.L.Jiang,
R.G.Gordley,
G.J.Jagadeesh,
J.E.Ladner,
G.Xiao,
M.Tordova,
G.L.Gilliland,
J.T.Stivers.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
The DNA repair enzyme uracil DNA glycosylase (UDG) pinches the phosphodiester
backbone of damaged DNA using the hydroxyl side chains of a conserved trio of
serine residues, resulting in flipping of the deoxyuridine from the DNA helix
into the enzyme active site. We have investigated the energetic role of these
serine-phosphodiester interactions using the complementary approaches of
crystallography, directed mutagenesis, and stereospecific phosphorothioate
substitutions. A new crystal structure of UDG bound to 5'-HO-dUAAp-3' (which
lacks the 5' phosphodiester group that interacts with the Ser88 pinching finger)
shows that the glycosidic bond of dU has been cleaved, and that the enzyme has
undergone the same specific clamping motion that brings key active site groups
into position as previously observed in the structures of human UDG bound to
large duplex DNA substrates. From this structure, it may be concluded that
glycosidic bond cleavage and the induced fit conformational change in UDG can
occur without the 5' pinching interaction. The S88A, S189A, and S192G "pinching"
mutations exhibit 360-, 80-, and 21-fold damaging effects on k(cat)/K(m),
respectively, while the S88A/S189A double mutant exhibits an 8200-fold damaging
effect. A free energy analysis of the combined effects of nonbridging
phosphorothioate substitution and mutation at these positions reveals the
presence of a modest amount of strain energy between the compressed 5' and 3'
phosphodiester groups flanking the bound uridine. Overall, these results
indicate a role for these serine-phosphodiester interactions in uracil flipping
and preorganization of the sugar ring into a reactive conformation. However, in
contrast to a recent proposal [Parikh, S. S., et al. (2000) Proc Natl. Acad.
Sci. 94, 5083], there is no evidence that conformational strain of the
glycosidic bond induced by serine pinching plays a major role in the 10(12)-fold
rate enhancement brought about by UDG.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
D.O.Zharkov,
G.V.Mechetin,
and
G.A.Nevinsky
(2010).
Uracil-DNA glycosylase: Structural, thermodynamic and kinetic aspects of lesion search and recognition.
|
| |
Mutat Res,
685,
11-20.
|
|
|
|
|
|
|
H.Hashimoto,
J.R.Horton,
X.Zhang,
and
X.Cheng
(2009).
UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications.
|
| |
Epigenetics,
4,
8.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
H.Hashimoto,
J.R.Horton,
X.Zhang,
M.Bostick,
S.E.Jacobsen,
and
X.Cheng
(2008).
The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix.
|
| |
Nature,
455,
826-829.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
P.Cysewski
(2008).
A post-SCF complete basis set study on the recognition patterns of uracil and cytosine by aromatic and pi-aromatic stacking interactions with amino acid residues.
|
| |
Phys Chem Chem Phys,
10,
2636-2645.
|
|
|
|
|
|
|
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.
|
| |
Acta Crystallogr D Biol Crystallogr,
64,
551-560.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
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.
|
| |
BMC Struct Biol,
7,
45.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
D.J.Krosky,
M.A.Bianchet,
L.Seiple,
S.Chung,
L.M.Amzel,
and
J.T.Stivers
(2006).
Mimicking damaged DNA with a small molecule inhibitor of human UNG2.
|
| |
Nucleic Acids Res,
34,
5872-5879.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.T.Stivers,
and
R.Nagarajan
(2006).
Probing enzyme phosphoester interactions by combining mutagenesis and chemical modification of phosphate ester oxygens.
|
| |
Chem Rev,
106,
3443-3467.
|
|
|
|
|
|
|
C.Cao,
Y.L.Jiang,
J.T.Stivers,
and
F.Song
(2004).
Dynamic opening of DNA during the enzymatic search for a damaged base.
|
| |
Nat Struct Mol Biol,
11,
1230-1236.
|
|
|
|
|
|
|
K.Kwon,
Y.L.Jiang,
and
J.T.Stivers
(2003).
Rational engineering of a DNA glycosylase specific for an unnatural cytosine:pyrene base pair.
|
| |
Chem Biol,
10,
351-359.
|
|
|
|
|
|
|
M.A.Bianchet,
L.A.Seiple,
Y.L.Jiang,
Y.Ichikawa,
L.M.Amzel,
and
J.T.Stivers
(2003).
Electrostatic guidance of glycosyl cation migration along the reaction coordinate of uracil DNA glycosylase.
|
| |
Biochemistry,
42,
12455-12460.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
N.Kato,
T.Kobayashi,
and
H.Honda
(2003).
Screening of stress enhancer based on analysis of gene expression profiles: enhancement of hyperthermia-induced tumor necrosis by an MMP-3 inhibitor.
|
| |
Cancer Sci,
94,
644-649.
|
|
|
|
|
|
|
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.
|
| |
J Biol Chem,
277,
19424-19432.
|
|
|
|
|
|
|
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.
|
| |
Acta Crystallogr D Biol Crystallogr,
58,
1269-1276.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
L.K.Zhang,
and
M.L.Gross
(2002).
Location of abasic sites in oligodeoxynucleotides by tandem mass spectrometry and by a chemical cleavage initiated by an unusual reaction of the ODN with MALDI matrix.
|
| |
J Am Soc Mass Spectrom,
13,
1418-1426.
|
|
|
|
|
|
|
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.
|
| |
Nucleic Acids Res,
30,
3086-3095.
|
|
|
|
|
|
|
R.Gilboa,
D.O.Zharkov,
G.Golan,
A.S.Fernandes,
S.E.Gerchman,
E.Matz,
J.H.Kycia,
A.P.Grollman,
and
G.Shoham
(2002).
Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA.
|
| |
J Biol Chem,
277,
19811-19816.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
Y.L.Jiang,
A.C.Drohat,
Y.Ichikawa,
and
J.T.Stivers
(2002).
Probing the limits of electrostatic catalysis by uracil DNA glycosylase using transition state mimicry and mutagenesis.
|
| |
J Biol Chem,
277,
15385-15392.
|
|
|
|
|
|
|
Y.L.Jiang,
and
J.T.Stivers
(2002).
Mutational analysis of the base-flipping mechanism of uracil DNA glycosylase.
|
| |
Biochemistry,
41,
11236-11247.
|
|
|
|
|
|
|
S.R.Bellamy,
and
G.S.Baldwin
(2001).
A kinetic analysis of substrate recognition by uracil-DNA glycosylase from herpes simplex virus type 1.
|
| |
Nucleic Acids Res,
29,
3857-3863.
|
|
|
|
|
|
|
Y.L.Jiang,
K.Kwon,
and
J.T.Stivers
(2001).
Turning On uracil-DNA glycosylase using a pyrene nucleotide switch.
|
| |
J Biol Chem,
276,
42347-42354.
|
|
|
|
|
|
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
codes are
shown on the right.
|
|
Links
