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PDBsum entry 1mud

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protein ligands links
Hydrolase PDB id
1mud
Jmol
Contents
Protein chain
225 a.a. *
Ligands
SF4
ADE ×2
GOL
Waters ×191
* Residue conservation analysis
PDB id:
1mud
Name: Hydrolase
Title: Catalytic domain of muty from escherichia coli, d138n mutant to adenine
Structure: Protein (adenine glycosylase). Chain: a. Fragment: catalytic domain. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562
Resolution:
1.80Å     R-factor:   0.192     R-free:   0.237
Authors: Y.Guan,J.A.Tainer
Key ref:
Y.Guan et al. (1998). MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily. Nat Struct Biol, 5, 1058-1064. PubMed id: 9846876 DOI: 10.1038/4168
Date:
20-Aug-98     Release date:   20-Sep-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P17802  (MUTY_ECOLI) -  A/G-specific adenine glycosylase
Seq:
Struc:
350 a.a.
225 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA repair   2 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
DOI no: 10.1038/4168 Nat Struct Biol 5:1058-1064 (1998)
PubMed id: 9846876  
 
 
MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily.
Y.Guan, R.C.Manuel, A.S.Arvai, S.S.Parikh, C.D.Mol, J.H.Miller, S.Lloyd, J.A.Tainer.
 
  ABSTRACT  
 
The DNA glycosylase MutY, which is a member of the Helix-hairpin-Helix (HhH) DNA glycosylase superfamily, excises adenine from mispairs with 8-oxoguanine and guanine. High-resolution crystal structures of the MutY catalytic core (cMutY), the complex with bound adenine, and designed mutants reveal the basis for adenine specificity and glycosyl bond cleavage chemistry. The two cMutY helical domains form a positively-charged groove with the adenine-specific pocket at their interface. The Watson-Crick hydrogen bond partners of the bound adenine are substituted by protein atoms, confirming a nucleotide flipping mechanism, and supporting a specific DNA binding orientation by MutY and structurally related DNA glycosylases.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. MutY active site, adenine binding, and proposed catalytic mechanism. a, Stereo 1.2 Å resolution electron density maps and the refined model for the [4Fe−4S] cluster region of D138N. The 2F[ o] - F[c] electron density is contoured at 10.0 (pink) and 1.5 (blue). b, Stereo F[o] - F[c] omit electron density for the cMutY-adenine complex showing the adenine binding site with 5.0 (pink) and 2.0 (blue) contours at 1.8 Å resolution. c, DNA glycosylation reaction schematic based upon the cMutY−adenine co-crystal structure and the D138N and E37S mutations. Asp 138 is positioned to abstract a proton from a bound water molecule, thus activating the water for attack on the C1' atom of the target adenine, while a protonated Glu 37 is positioned to stabilize the developing transition state through a hydrogen bond to adenine N7, facilitating bond cleavage. A subsequent, uncoupled lyase activity may arise through the action of Lys 142.
Figure 4.
Figure 4. MutY adenine specificity and DNA binding with implications for the HhH glycosylase superfamily. a, MutY domain interface and bound adenine (white, carbons; blue, nitrogens) in the base-specificity pocket with the side chains of Asn 138, Glu 37, Leu 40, Gln 42, Val 45, Met 185, Ser 120, Gln 182 and Arg 194 shown in ball and stick (pink bonds and polar atom-colored spheres, with residues labeled). The orientation and ribbon coloring are the same as in Fig. 2a. b, The orientation of DNA binding to MutY supported by the adenine and Asp 138 positions. DNA with a flipped-out nucleotide from the UDG−DNA complex^22 matches the MutY groove bend when positioned as required to match the adenine (middle, pink) and catalytically appropriate Asp 138 positions. This proposed model furthermore places the HhH motif (purple) for backbone recognition and provides positive electrostatic complementarity (blue surface) for the DNA phosphates.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1998, 5, 1058-1064) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21220122 B.Dalhus, M.Forsbring, I.H.Helle, E.S.Vik, R.J.Forstrøm, P.H.Backe, I.Alseth, and M.Bjørås (2011).
Separation-of-function mutants unravel the dual-reaction mode of human 8-oxoguanine DNA glycosylase.
  Structure, 19, 117-127.
PDB code: 2xhi
20725929 A.A.Out, C.M.Tops, M.Nielsen, M.M.Weiss, I.J.van Minderhout, I.F.Fokkema, M.P.Buisine, K.Claes, C.Colas, R.Fodde, F.Fostira, P.F.Franken, M.Gaustadnes, K.Heinimann, S.V.Hodgson, F.B.Hogervorst, E.Holinski-Feder, K.Lagerstedt-Robinson, S.Olschwang, A.M.van den Ouweland, E.J.Redeker, R.J.Scott, B.Vankeirsbilck, R.V.Grønlund, J.T.Wijnen, F.P.Wikman, S.Aretz, J.R.Sampson, P.Devilee, J.T.den Dunnen, and F.J.Hes (2010).
Leiden Open Variation Database of the MUTYH gene.
  Hum Mutat, 31, 1205-1215.  
20628285 F.Fostira, C.Papademitriou, A.Efremidis, and D.Yannoukakos (2010).
An in-frame exon-skipping MUTYH mutation is associated with early-onset colorectal cancer.
  Dis Colon Rectum, 53, 1197-1201.  
  20944229 G.W.Han, X.L.Yang, D.McMullan, Y.E.Chong, S.S.Krishna, C.L.Rife, D.Weekes, S.M.Brittain, P.Abdubek, E.Ambing, T.Astakhova, H.L.Axelrod, D.Carlton, J.Caruthers, H.J.Chiu, T.Clayton, L.Duan, J.Feuerhelm, J.C.Grant, S.K.Grzechnik, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, A.Kumar, D.Marciano, M.D.Miller, A.T.Morse, E.Nigoghossian, L.Okach, J.Paulsen, R.Reyes, H.van den Bedem, A.White, G.Wolf, Q.Xu, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, M.A.Elsliger, P.Schimmel, and I.A.Wilson (2010).
Structure of a tryptophanyl-tRNA synthetase containing an iron-sulfur cluster.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1326-1334.
PDB code: 2g36
20047321 J.C.Genereux, A.K.Boal, and J.K.Barton (2010).
DNA-mediated charge transport in redox sensing and signaling.
  J Am Chem Soc, 132, 891-905.  
  20809962 K.Jansson, A.Blomberg, P.Sunnerhagen, and M.Alm Rosenblad (2010).
Evolutionary loss of 8-oxo-G repair components among eukaryotes.
  Genome Integr, 1, 12.  
19899172 M.V.Kumar, and R.Swaminathan (2010).
A novel approach to segregate and identify functional loop regions in protein structures using their Ramachandran maps.
  Proteins, 78, 900-916.  
20974931 Y.G.Mok, R.Uzawa, J.Lee, G.M.Weiner, B.F.Eichman, R.L.Fischer, and J.H.Huh (2010).
Domain structure of the DEMETER 5-methylcytosine DNA glycosylase.
  Proc Natl Acad Sci U S A, 107, 19225-19230.  
19129187 J.T.Yeeles, R.Cammack, and M.S.Dillingham (2009).
An Iron-Sulfur Cluster Is Essential for the Binding of Broken DNA by AddAB-type Helicase-Nucleases.
  J Biol Chem, 284, 7746-7755.  
19523222 P.W.Chang, A.Madabushi, and A.L.Lu (2009).
Insights into the role of Val45 and Gln182 of Escherichia coli MutY in DNA substrate binding and specificity.
  BMC Biochem, 10, 19.  
19836313 S.Kundu, M.K.Brinkmeyer, A.L.Livingston, and S.S.David (2009).
Adenine removal activity and bacterial complementation with the human MutY homologue (MUTYH) and Y165C, G382D, P391L and Q324R variants associated with colorectal cancer.
  DNA Repair (Amst), 8, 1400-1410.  
19841264 S.Lee, and G.L.Verdine (2009).
Atomic substitution reveals the structural basis for substrate adenine recognition and removal by adenine DNA glycosylase.
  Proc Natl Acad Sci U S A, 106, 18497-18502.
PDB code: 3g0q
19200715 S.Schneider, S.Schorr, and T.Carell (2009).
Crystal structure analysis of DNA lesion repair and tolerance mechanisms.
  Curr Opin Struct Biol, 19, 87-95.  
19099189 Y.Wu, A.N.Suhasini, and R.M.Brosh (2009).
Welcome the family of FANCJ-like helicases to the block of genome stability maintenance proteins.
  Cell Mol Life Sci, 66, 1209-1222.  
19519404 Y.Wu, and R.M.Brosh (2009).
FANCJ helicase operates in the Fanconi Anemia DNA repair pathway and the response to replicational stress.
  Curr Mol Med, 9, 470-482.  
18682218 B.R.Bowman, S.Lee, S.Wang, and G.L.Verdine (2008).
Structure of the E. coli DNA glycosylase AlkA bound to the ends of duplex DNA: a system for the structure determination of lesion-containing DNA.
  Structure, 16, 1166-1174.
PDB codes: 3cvs 3cvt 3cw7 3cwa 3cws 3cwt 3cwu
18534194 M.Ali, H.Kim, S.Cleary, C.Cupples, S.Gallinger, and R.Bristow (2008).
Characterization of mutant MUTYH proteins associated with familial colorectal cancer.
  Gastroenterology, 135, 499-507.  
18166975 M.L.Hegde, T.K.Hazra, and S.Mitra (2008).
Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells.
  Cell Res, 18, 27-47.  
19506731 M.L.Poulsen, and M.L.Bisgaard (2008).
MUTYH Associated Polyposis (MAP).
  Curr Genomics, 9, 420-435.  
18029358 R.A.Pugh, M.Honda, H.Leesley, A.Thomas, Y.Lin, M.J.Nilges, I.K.Cann, and M.Spies (2008).
The iron-containing domain is essential in Rad3 helicases for coupling of ATP hydrolysis to DNA translocation and for targeting the helicase to the single-stranded DNA-double-stranded DNA junction.
  J Biol Chem, 283, 1732-1743.  
18578568 S.C.Wolski, J.Kuper, P.Hänzelmann, J.J.Truglio, D.L.Croteau, B.Van Houten, and C.Kisker (2008).
Crystal structure of the FeS cluster-containing nucleotide excision repair helicase XPD.
  PLoS Biol, 6, e149.
PDB code: 2vsf
17989957 S.Kulick, C.Moccia, C.Kraft, and S.Suerbaum (2008).
The Helicobacter pylori mutY homologue HP0142 is an antimutator gene that prevents specific C to A transversions.
  Arch Microbiol, 189, 263-270.  
17410210 A.H.Metz, T.Hollis, and B.F.Eichman (2007).
DNA damage recognition and repair by 3-methyladenine DNA glycosylase I (TAG).
  EMBO J, 26, 2411-2420.
PDB codes: 2ofi 2ofk
17599416 A.K.Boal, E.Yavin, and J.K.Barton (2007).
DNA repair glycosylases with a [4Fe-4S] cluster: a redox cofactor for DNA-mediated charge transport?
  J Inorg Biochem, 101, 1913-1921.  
17893144 B.E.Weiner, H.Huang, B.M.Dattilo, M.J.Nilges, E.Fanning, and W.J.Chazin (2007).
An iron-sulfur cluster in the C-terminal domain of the p58 subunit of human DNA primase.
  J Biol Chem, 282, 33444-33451.  
17114250 H.Bai, and A.L.Lu (2007).
Physical and functional interactions between Escherichia coli MutY glycosylase and mismatch repair protein MutS.
  J Bacteriol, 189, 902-910.  
17715144 S.Couvé-Privat, G.Macé, F.Rosselli, and M.K.Saparbaev (2007).
Psoralen-induced DNA adducts are substrates for the base excision repair pathway in human cells.
  Nucleic Acids Res, 35, 5672-5682.  
17141577 S.F.Holmes, K.D.Scarpinato, S.D.McCulloch, R.M.Schaaper, and T.A.Kunkel (2007).
Specialized mismatch repair function of Glu339 in the Phe-X-Glu motif of yeast Msh6.
  DNA Repair (Amst), 6, 293-303.  
17581577 S.S.David, V.L.O'Shea, and S.Kundu (2007).
Base-excision repair of oxidative DNA damage.
  Nature, 447, 941-950.  
17855402 X.Guan, A.Madabushi, D.Y.Chang, M.E.Fitzgerald, G.Shi, A.C.Drohat, and A.L.Lu (2007).
The human checkpoint sensor Rad9-Rad1-Hus1 interacts with and stimulates DNA repair enzyme TDG glycosylase.
  Nucleic Acids Res, 35, 6207-6218.  
16287072 A.M.Russell, J.Zhang, J.Luz, P.Hutter, P.O.Chappuis, C.R.Berthod, P.Maillet, H.Mueller, and K.Heinimann (2006).
Prevalence of MYH germline mutations in Swiss APC mutation-negative polyposis patients.
  Int J Cancer, 118, 1937-1940.  
16505354 E.Yavin, E.D.Stemp, V.L.O'shea, S.S.David, and J.K.Barton (2006).
Electron trap for DNA-bound repair enzymes: a strategy for DNA-mediated signaling.
  Proc Natl Acad Sci U S A, 103, 3610-3614.  
16292541 L.M.Baudhuin, L.R.Roberts, F.T.Enders, R.L.Swanson, T.A.Mettler, I.Aderca, L.M.Stadheim, and W.E.Highsmith (2006).
MYH Y165C and G382D mutations in hepatocellular carcinoma and cholangiocarcinoma patients.
  J Cancer Res Clin Oncol, 132, 159-162.  
16453120 P.M.Rodrigues, A.L.Macedo, B.J.Goodfellow, I.Moura, and J.J.Moura (2006).
Desulfovibrio gigas ferredoxin II: redox structural modulation of the [3Fe-4S] cluster.
  J Biol Inorg Chem, 11, 307-315.  
17115714 R.K.Walker, A.K.McCullough, and R.S.Lloyd (2006).
Uncoupling of nucleotide flipping and DNA bending by the t4 pyrimidine dimer DNA glycosylase.
  Biochemistry, 45, 14192-14200.  
16768442 T.Christian, C.Evilia, and Y.M.Hou (2006).
Catalysis by the second class of tRNA(m1G37) methyl transferase requires a conserved proline.
  Biochemistry, 45, 7463-7473.  
15952888 D.C.Johnson, D.R.Dean, A.D.Smith, and M.K.Johnson (2005).
Structure, function, and formation of biological iron-sulfur clusters.
  Annu Rev Biochem, 74, 247-281.  
15738421 E.Yavin, A.K.Boal, E.D.Stemp, E.M.Boon, A.L.Livingston, V.L.O'Shea, S.S.David, and J.K.Barton (2005).
Protein-DNA charge transport: redox activation of a DNA repair protein by guanine radical.
  Proc Natl Acad Sci U S A, 102, 3546-3551.  
15642264 G.M.Lingaraju, A.A.Sartori, D.Kostrewa, A.E.Prota, J.Jiricny, and F.K.Winkler (2005).
A DNA glycosylase from Pyrobaculum aerophilum with an 8-oxoguanine binding mode and a noncanonical helix-hairpin-helix structure.
  Structure, 13, 87-98.
PDB codes: 1xqo 1xqp
15673720 H.Bai, S.Jones, X.Guan, T.M.Wilson, J.R.Sampson, J.P.Cheadle, and A.L.Lu (2005).
Functional characterization of two human MutY homolog (hMYH) missense mutations (R227W and V232F) that lie within the putative hMSH6 binding domain and are associated with hMYH polyposis.
  Nucleic Acids Res, 33, 597-604.  
15811798 O.A.Lukianova, and S.S.David (2005).
A role for iron-sulfur clusters in DNA repair.
  Curr Opin Chem Biol, 9, 145-151.  
15805527 T.Davidsen, M.Bjørås, E.C.Seeberg, and T.Tønjum (2005).
Antimutator role of DNA glycosylase MutY in pathogenic Neisseria species.
  J Bacteriol, 187, 2801-2809.  
16096281 T.Watanabe, J.O.Blaisdell, S.S.Wallace, and J.P.Bond (2005).
Engineering functional changes in Escherichia coli endonuclease III based on phylogenetic and structural analyses.
  J Biol Chem, 280, 34378-34384.  
15681617 Y.Ushijima, Y.Tominaga, T.Miura, D.Tsuchimoto, K.Sakumi, and Y.Nakabeppu (2005).
A functional analysis of the DNA glycosylase activity of mouse MUTYH protein excising 2-hydroxyadenine opposite guanine in DNA.
  Nucleic Acids Res, 33, 672-682.  
14742662 A.Ichinoe, M.Behmanesh, Y.Tominaga, Y.Ushijima, S.Hirano, Y.Sakai, D.Tsuchimoto, K.Sakumi, N.Wake, and Y.Nakabeppu (2004).
Identification and characterization of two forms of mouse MUTYH proteins encoded by alternatively spliced transcripts.
  Nucleic Acids Res, 32, 477-487.  
15116069 B.I.Lee, K.H.Kim, S.J.Park, S.H.Eom, H.K.Song, and S.W.Suh (2004).
Ring-shaped architecture of RecR: implications for its role in homologous recombinational DNA repair.
  EMBO J, 23, 2029-2038.
PDB code: 1vdd
15456766 C.Y.Lee, H.Bai, R.Houle, G.M.Wilson, and A.L.Lu (2004).
An Escherichia coli MutY mutant without the six-helix barrel domain is a dimer in solution and assembles cooperatively into multisubunit complexes with DNA.
  J Biol Chem, 279, 52653-52663.  
15310837 H.Ma, H.M.Lee, and E.W.Englander (2004).
N-terminus of the rat adenine glycosylase MYH affects excision rates and processing of MYH-generated abasic sites.
  Nucleic Acids Res, 32, 4332-4339.  
15356290 H.P.Shanahan, M.A.Garcia, S.Jones, and J.M.Thornton (2004).
Identifying DNA-binding proteins using structural motifs and the electrostatic potential.
  Nucleic Acids Res, 32, 4732-4741.  
14961129 J.C.Fromme, A.Banerjee, S.J.Huang, and G.L.Verdine (2004).
Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase.
  Nature, 427, 652-656.
PDB codes: 1rrq 1rrs 1rrt 1vrl
15494448 K.Hashiguchi, J.A.Stuart, N.C.de Souza-Pinto, and V.A.Bohr (2004).
The C-terminal alphaO helix of human Ogg1 is essential for 8-oxoguanine DNA glycosylase activity: the mitochondrial beta-Ogg1 lacks this domain and does not have glycosylase activity.
  Nucleic Acids Res, 32, 5596-5608.  
15236166 L.Wang, L.M.Baudhuin, L.A.Boardman, K.J.Steenblock, G.M.Petersen, K.C.Halling, A.J.French, R.A.Johnson, L.J.Burgart, K.Rabe, N.M.Lindor, and S.N.Thibodeau (2004).
MYH mutations in patients with attenuated and classic polyposis and with young-onset colorectal cancer without polyps.
  Gastroenterology, 127, 9.  
15326180 R.C.Manuel, K.Hitomi, A.S.Arvai, P.G.House, A.J.Kurtz, M.L.Dodson, A.K.McCullough, J.A.Tainer, and R.S.Lloyd (2004).
Reaction intermediates in the catalytic mechanism of Escherichia coli MutY DNA glycosylase.
  J Biol Chem, 279, 46930-46939.
PDB codes: 1wef 1weg 1wei
15128940 Y.Choi, J.J.Harada, R.B.Goldberg, and R.L.Fischer (2004).
An invariant aspartic acid in the DNA glycosylase domain of DEMETER is necessary for transcriptional activation of the imprinted MEDEA gene.
  Proc Natl Acad Sci U S A, 101, 7481-7486.  
15199168 Y.Tominaga, Y.Ushijima, D.Tsuchimoto, M.Mishima, M.Shirakawa, S.Hirano, K.Sakumi, and Y.Nakabeppu (2004).
MUTYH prevents OGG1 or APEX1 from inappropriately processing its substrate or reaction product with its C-terminal domain.
  Nucleic Acids Res, 32, 3198-3211.  
12667065 A.L.Lu, and P.M.Wright (2003).
Characterization of an Escherichia coli mutant MutY with a cysteine to alanine mutation at the iron-sulfur cluster domain.
  Biochemistry, 42, 3742-3750.  
14517230 B.F.Eichman, E.J.O'Rourke, J.P.Radicella, and T.Ellenberger (2003).
Crystal structures of 3-methyladenine DNA glycosylase MagIII and the recognition of alkylated bases.
  EMBO J, 22, 4898-4909.
PDB codes: 1pu6 1pu7 1pu8
12600940 B.R.Szymczyna, J.Bowman, S.McCracken, A.Pineda-Lucena, Y.Lu, B.Cox, M.Lambermon, B.R.Graveley, C.H.Arrowsmith, and B.J.Blencowe (2003).
Structure and function of the PWI motif: a novel nucleic acid-binding domain that facilitates pre-mRNA processing.
  Genes Dev, 17, 461-475.
PDB code: 1mp1
13129925 C.Cao, K.Kwon, Y.L.Jiang, A.C.Drohat, and J.T.Stivers (2003).
Solution structure and base perturbation studies reveal a novel mode of alkylated base recognition by 3-methyladenine DNA glycosylase I.
  J Biol Chem, 278, 48012-48020.
PDB code: 1p7m
14559969 E.M.Boon, A.L.Livingston, N.H.Chmiel, S.S.David, and J.K.Barton (2003).
DNA-mediated charge transport for DNA repair.
  Proc Natl Acad Sci U S A, 100, 12543-12547.  
12766151 J.A.McCann, and P.J.Berti (2003).
Adenine release is fast in MutY-catalyzed hydrolysis of G:A and 8-Oxo-G:A DNA mismatches.
  J Biol Chem, 278, 29587-29592.  
12840008 J.C.Fromme, and G.L.Verdine (2003).
Structure of a trapped endonuclease III-DNA covalent intermediate.
  EMBO J, 22, 3461-3471.
PDB codes: 1orn 1orp 1p59
12799430 L.Li, and A.L.Lu (2003).
The C-terminal domain of Escherichia coli MutY is involved in DNA binding and glycosylase activities.
  Nucleic Acids Res, 31, 3038-3049.  
12456671 P.Wu, C.Qiu, A.Sohail, X.Zhang, A.S.Bhagwat, and X.Cheng (2003).
Mismatch repair in methylated DNA. Structure and activity of the mismatch-specific thymine glycosylase domain of methyl-CpG-binding protein MBD4.
  J Biol Chem, 278, 5285-5291.
PDB code: 1ngn
12161745 A.C.Drohat, K.Kwon, D.J.Krosky, and J.T.Stivers (2002).
3-Methyladenine DNA glycosylase I is an unexpected helix-hairpin-helix superfamily member.
  Nat Struct Biol, 9, 659-664.
PDB code: 1lmz
11964390 A.S.Bernards, J.K.Miller, K.K.Bao, and I.Wong (2002).
Flipping duplex DNA inside out: a double base-flipping reaction mechanism by Escherichia coli MutY adenine glycosylase.
  J Biol Chem, 277, 20960-20964.  
  12426118 C.J.Burrows, J.G.Muller, O.Kornyushyna, W.Luo, V.Duarte, M.D.Leipold, and S.S.David (2002).
Structure and potential mutagenicity of new hydantoin products from guanosine and 8-oxo-7,8-dihydroguanine oxidation by transition metals.
  Environ Health Perspect, 110, 713-717.  
12057763 D.O.Zharkov, and A.P.Grollman (2002).
Combining structural and bioinformatics methods for the analysis of functionally important residues in DNA glycosylases.
  Free Radic Biol Med, 32, 1254-1263.  
12081496 E.M.Boon, M.A.Pope, S.D.Williams, S.S.David, and J.K.Barton (2002).
DNA-mediated charge transport as a probe of MutY/DNA interaction.
  Biochemistry, 41, 8464-8470.  
12055620 J.C.Fromme, and G.L.Verdine (2002).
Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM.
  Nat Struct Biol, 9, 544-552.
PDB codes: 1l1t 1l1z 1l2b 1l2c 1l2d
12198481 K.S.Yan, and M.M.Zhou (2002).
TAGging the target for damage control.
  Nat Struct Biol, 9, 638-640.  
11960995 M.A.Pope, S.L.Porello, and S.S.David (2002).
Escherichia coli apurinic-apyrimidinic endonucleases enhance the turnover of the adenine glycosylase MutY with G:A substrates.
  J Biol Chem, 277, 22605-22615.  
11818965 N.Al-Tassan, N.H.Chmiel, J.Maynard, N.Fleming, A.L.Livingston, G.T.Williams, A.K.Hodges, D.R.Davies, S.S.David, J.R.Sampson, and J.P.Cheadle (2002).
Inherited variants of MYH associated with somatic G:C-->T:A mutations in colorectal tumors.
  Nat Genet, 30, 227-232.  
11900536 T.E.Messick, N.H.Chmiel, M.P.Golinelli, M.R.Langer, L.Joshua-Tor, and S.S.David (2002).
Noncysteinyl coordination to the [4Fe-4S]2+ cluster of the DNA repair adenine glycosylase MutY introduced via site-directed mutagenesis. Structural characterization of an unusual histidinyl-coordinated cluster.
  Biochemistry, 41, 3931-3942.
PDB code: 1kqj
12000829 V.Starkuviene, and H.J.Fritz (2002).
A novel type of uracil-DNA glycosylase mediating repair of hydrolytic DNA damage in the extremely thermophilic eubacterium Thermus thermophilus.
  Nucleic Acids Res, 30, 2097-2102.  
11801590 Y.Gu, A.Parker, T.M.Wilson, H.Bai, D.Y.Chang, and A.L.Lu (2002).
Human MutY homolog, a DNA glycosylase involved in base excision repair, physically and functionally interacts with mismatch repair proteins human MutS homolog 2/human MutS homolog 6.
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12220190 Y.L.Jiang, J.T.Stivers, and F.Song (2002).
Base-flipping mutations of uracil DNA glycosylase: substrate rescue using a pyrene nucleotide wedge.
  Biochemistry, 41, 11248-11254.  
11788726 Y.N.Fondufe-Mittendorf, C.Härer, W.Kramer, and H.J.Fritz (2002).
Two amino acid replacements change the substrate preference of DNA mismatch glycosylase Mig.MthI from T/G to A/G.
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11160880 H.Yang, I.T.Phan, S.Fitz-Gibbon, M.K.Shivji, R.D.Wood, W.M.Clendenin, E.C.Hyman, and J.H.Miller (2001).
A thermostable endonuclease III homolog from the archaeon Pyrobaculum aerophilum.
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11160897 H.Yang, W.M.Clendenin, D.Wong, B.Demple, M.M.Slupska, J.H.Chiang, and J.H.Miller (2001).
Enhanced activity of adenine-DNA glycosylase (Myh) by apurinic/apyrimidinic endonuclease (Ape1) in mammalian base excision repair of an A/GO mismatch.
  Nucleic Acids Res, 29, 743-752.  
11139626 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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11223884 O.D.Schärer, and J.Jiricny (2001).
Recent progress in the biology, chemistry and structural biology of DNA glycosylases.
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11504879 S.T.Hoehn, C.J.Turner, and J.Stubbe (2001).
Solution structure of an oligonucleotide containing an abasic site: evidence for an unusual deoxyribose conformation.
  Nucleic Acids Res, 29, 3413-3423.
PDB codes: 1g5d 1g5e 1giz 1gj0
11557810 X.Cheng, and R.J.Roberts (2001).
AdoMet-dependent methylation, DNA methyltransferases and base flipping.
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11591657 X.Li, and A.L.Lu (2001).
Molecular cloning and functional analysis of the MutY homolog of Deinococcus radiodurans.
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10813834 A.Gogos, D.Jantz, S.Sentürker, D.Richardson, M.Dizdaroglu, and N.D.Clarke (2000).
Assignment of enzyme substrate specificity by principal component analysis of aligned protein sequences: an experimental test using DNA glycosylase homologs.
  Proteins, 40, 98.  
11058099 A.J.Doherty, and S.W.Suh (2000).
Structural and mechanistic conservation in DNA ligases.
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10954587 A.Parker, Y.Gu, and A.L.Lu (2000).
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11101292 D.O.Zharkov, R.Gilboa, I.Yagil, J.H.Kycia, S.E.Gerchman, G.Shoham, and A.P.Grollman (2000).
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11329883 H.Kamiya, and H.Kasai (2000).
2-hydroxyadenine in DNA is a very poor substrate of the Escherichia coli MutY protein.
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10671447 H.Yang, S.Fitz-Gibbon, E.M.Marcotte, J.H.Tai, E.C.Hyman, and J.H.Miller (2000).
Characterization of a thermostable DNA glycosylase specific for U/G and T/G mismatches from the hyperthermophilic archaeon Pyrobaculum aerophilum.
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10698952 J.Y.Lee, C.Chang, H.K.Song, J.Moon, J.K.Yang, H.K.Kim, S.T.Kwon, and S.W.Suh (2000).
Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications.
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PDB codes: 1dgs 1dgt 1v9p
10921868 M.Sugahara, T.Mikawa, T.Kumasaka, M.Yamamoto, R.Kato, K.Fukuyama, Y.Inoue, and S.Kuramitsu (2000).
Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile, Thermus thermophilus HB8.
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PDB code: 1ee8
10660595 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).
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12760025 S.D.Bruner, D.P.Norman, J.C.Fromme, and G.L.Verdine (2000).
Structural and mechanistic studies on repair of 8-oxoguanine in mammalian cells.
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10955998 S.D.Williams, and S.S.David (2000).
A single engineered point mutation in the adenine glycosylase MutY confers bifunctional glycosylase/AP lyase activity.
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10924106 T.C.Umland, S.Q.Wei, R.Craigie, and D.R.Davies (2000).
Structural basis of DNA bridging by barrier-to-autointegration factor.
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PDB code: 1ci4
10675345 T.Hollis, Y.Ichikawa, and T.Ellenberger (2000).
DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA.
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PDB code: 1diz
11095667 X.Li, and A.L.Lu (2000).
Intact MutY and its catalytic domain differentially contact with A/8-oxoG-containing DNA.
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The C-terminal domain of MutY glycosylase determines the 7,8-dihydro-8-oxo-guanine specificity and is crucial for mutation avoidance.
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10908318 X.Shao, and N.V.Grishin (2000).
Common fold in helix-hairpin-helix proteins.
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Initiation of base excision repair: glycosylase mechanisms and structures.
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10467137 A.Shekhtman, L.McNaughton, R.P.Cunningham, and S.M.Baxter (1999).
Identification of the Archaeoglobus fulgidus endonuclease III DNA interaction surface using heteronuclear NMR methods.
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DNA repair mechanisms for the recognition and removal of damaged DNA bases.
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Substrate recognition by Escherichia coli MutY using substrate analogs.
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Functional expression of hMYH, a human homolog of the Escherichia coli MutY protein.
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The active site of the Escherichia coli MutY DNA adenine glycosylase.
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10047578 S.S.Parikh, C.D.Mol, D.J.Hosfield, and J.A.Tainer (1999).
Envisioning the molecular choreography of DNA base excision repair.
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A new member of the endonuclease III family of DNA repair enzymes that removes methylated purines from DNA.
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