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PDBsum entry 1l2d

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protein dna_rna metals links
Hydrolase/DNA PDB id
1l2d
Jmol
Contents
Protein chain
259 a.a. *
DNA/RNA
Metals
_ZN
Waters ×181
* Residue conservation analysis
PDB id:
1l2d
Name: Hydrolase/DNA
Title: Mutm (fpg)-DNA estranged guanine mismatch recognition complex
Structure: 5'- d( Ap G Gp Tp Ap Gp Ap Cp Gp Tp Gp Gp Ap Cp Gp C)-3'. Chain: b. Engineered: yes. 5'-d( Tp Gp C Gp Tp Cp Cp Ap (Hpd) p Gp Tp Cp Tp Ap Cp C)-3'. Chain: c. Engineered: yes. Mutm.
Source: Synthetic: yes. Geobacillus stearothermophilus. Organism_taxid: 1422. Gene: mutm. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Trimer (from PQS)
Resolution:
2.00Å     R-factor:   0.217     R-free:   0.251
Authors: J.C.Fromme,G.L.Verdine
Key ref:
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. PubMed id: 12055620 DOI: 10.1038/nsb809
Date:
20-Feb-02     Release date:   14-Jun-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
No UniProt id for this chain
Struc: 259 a.a.
Key:    Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA repair   3 terms 
  Biochemical function     catalytic activity     8 terms  

 

 
DOI no: 10.1038/nsb809 Nat Struct Biol 9:544-552 (2002)
PubMed id: 12055620  
 
 
Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM.
J.C.Fromme, G.L.Verdine.
 
  ABSTRACT  
 
MutM is a bacterial 8-oxoguanine glycosylase responsible for initiating base-excision repair of oxidized guanine residues in DNA. Here we report five different crystal structures of MutM-DNA complexes that represent different steps of the repair reaction cascade catalyzed by the protein and also differ in the identity of the base opposite the lesion (the 'estranged' base). These structures reveal that the MutM active site performs the multiple steps of base-excision and 3' and 5' nicking with minimal rearrangement of the DNA backbone.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Comparison of active sites from three different stages of catalysis. a, Active site structure of the rAb C recognition complex 6. The density corresponding to the C1' atom and its hydroxyl is weak, presumably owing to several rotamers about the C2'-C3' bond.
Figure 4.
Figure 4. Recognition of the estranged base by MutM. a, Recognition in the rAb C complex. b, Recognition in the rAb G complex. c, Recognition in the rAb T complex. Dashes indicate hydrogen bonds, and red circles denote a van der Waals interaction. d−f, Structural formulae schematics of the mode of recognition seen in (a−c), respectively.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2002, 9, 544-552) copyright 2002.  
  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
20031487 Y.Guo, V.Bandaru, P.Jaruga, X.Zhao, C.J.Burrows, S.Iwai, M.Dizdaroglu, J.P.Bond, and S.S.Wallace (2010).
The oxidative DNA glycosylases of Mycobacterium tuberculosis exhibit different substrate preferences from their Escherichia coli counterparts.
  DNA Repair (Amst), 9, 177-190.  
19889642 Y.Qi, M.C.Spong, K.Nam, M.Karplus, and G.L.Verdine (2010).
Entrapment and structure of an extrahelical guanine attempting to enter the active site of a bacterial DNA glycosylase, MutM.
  J Biol Chem, 285, 1468-1478.
PDB codes: 3jr4 3jr5
19151100 H.Sanada, T.Nakanishi, H.Inoue, and M.Kitamura (2009).
Cloning and expression of the MutM gene from obligate anaerobic bacterium Desulfovibrio vulgaris (Miyazaki F).
  J Biochem, 145, 525-532.  
19625256 K.Imamura, S.S.Wallace, and S.Doublié (2009).
Structural characterization of a viral NEIL1 ortholog unliganded and bound to abasic site-containing DNA.
  J Biol Chem, 284, 26174-26183.
PDB codes: 3a42 3a45 3a46
19134198 K.L.Tibballs, O.H.Ambur, K.Alfsnes, H.Homberset, S.A.Frye, T.Davidsen, and T.Tønjum (2009).
Characterization of the meningococcal DNA glycosylase Fpg involved in base excision repair.
  BMC Microbiol, 9, 7.  
19217358 S.D.Kathe, R.Barrantes-Reynolds, P.Jaruga, M.R.Newton, C.J.Burrows, V.Bandaru, M.Dizdaroglu, J.P.Bond, and S.S.Wallace (2009).
Plant and fungal Fpg homologs are formamidopyrimidine DNA glycosylases but not 8-oxoguanine DNA glycosylases.
  DNA Repair (Amst), 8, 643-653.  
  20157476 S.Shi, J.Pei, R.I.Sadreyev, L.N.Kinch, I.Majumdar, J.Tong, H.Cheng, B.H.Kim, and N.V.Grishin (2009).
Analysis of CASP8 targets, predictions and assessment methods.
  Database (Oxford), 2009, bap003.  
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
18506863 H.Mueller, M.Hopfinger, and T.Carell (2008).
Synthesis of a stabilized version of the imidazolone DNA lesion.
  Chembiochem, 9, 1617-1622.  
18072751 J.C.Delaney, and J.M.Essigmann (2008).
Biological properties of single chemical-DNA adducts: a twenty year perspective.
  Chem Res Toxicol, 21, 232-252.  
18557781 V.S.Sidorenko, G.V.Mechetin, G.A.Nevinsky, and D.O.Zharkov (2008).
Ionic strength and magnesium affect the specificity of Escherichia coli and human 8-oxoguanine-DNA glycosylases.
  FEBS J, 275, 3747-3760.  
17090545 N.A.Kuznetsov, V.V.Koval, G.A.Nevinsky, K.T.Douglas, D.O.Zharkov, and O.S.Fedorova (2007).
Kinetic conformational analysis of human 8-oxoguanine-DNA glycosylase.
  J Biol Chem, 282, 1029-1038.  
16497933 A.Banerjee, W.L.Santos, and G.L.Verdine (2006).
Structure of a DNA glycosylase searching for lesions.
  Science, 311, 1153-1157.
PDB codes: 2f5n 2f5o 2f5p 2f5q 2f5s
17002303 K.Y.Kropachev, D.O.Zharkov, and A.P.Grollman (2006).
Catalytic mechanism of Escherichia coli endonuclease VIII: roles of the intercalation loop and the zinc finger.
  Biochemistry, 45, 12039-12049.  
16928690 M.Rogacheva, A.Ishchenko, M.Saparbaev, S.Kuznetsova, and V.Ogryzko (2006).
High resolution characterization of formamidopyrimidine-DNA glycosylase interaction with its substrate by chemical cross-linking and mass spectrometry using substrate analogs.
  J Biol Chem, 281, 32353-32365.  
16585517 P.C.Blainey, A.M.van Oijen, A.Banerjee, G.L.Verdine, and X.S.Xie (2006).
A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA.
  Proc Natl Acad Sci U S A, 103, 5752-5757.  
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.  
16145054 G.Golan, D.O.Zharkov, H.Feinberg, A.S.Fernandes, E.I.Zaika, J.H.Kycia, A.P.Grollman, and G.Shoham (2005).
Structure of the uncomplexed DNA repair enzyme endonuclease VIII indicates significant interdomain flexibility.
  Nucleic Acids Res, 33, 5006-5016.
PDB codes: 1q39 1q3b 1q3c
15814814 J.G.Renisio, S.Cosquer, I.Cherrak, S.El Antri, O.Mauffret, and S.Fermandjian (2005).
Pre-organized structure of viral DNA at the binding-processing site of HIV-1 integrase.
  Nucleic Acids Res, 33, 1970-1981.
PDB code: 1tqr
16243784 K.Pereira de Jésus, L.Serre, C.Zelwer, and B.Castaing (2005).
Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA.
  Nucleic Acids Res, 33, 5936-5944.
PDB codes: 1nnj 1pji 1pjj 1pm5
15210696 B.B.Hopkins, and N.O.Reich (2004).
Simultaneous DNA binding, bending, and base flipping: evidence for a novel M.EcoRI methyltransferase-DNA complex.
  J Biol Chem, 279, 37049-37060.  
14607836 E.I.Zaika, R.A.Perlow, E.Matz, S.Broyde, R.Gilboa, A.P.Grollman, and D.O.Zharkov (2004).
Substrate discrimination by formamidopyrimidine-DNA glycosylase: a mutational analysis.
  J Biol Chem, 279, 4849-4861.  
15249553 F.Coste, M.Ober, T.Carell, S.Boiteux, C.Zelwer, and B.Castaing (2004).
Structural basis for the recognition of the FapydG lesion (2,6-diamino-4-hydroxy-5-formamidopyrimidine) by formamidopyrimidine-DNA glycosylase.
  J Biol Chem, 279, 44074-44083.
PDB codes: 1tdz 1xc8
15102448 J.C.Fromme, A.Banerjee, and G.L.Verdine (2004).
DNA glycosylase recognition and catalysis.
  Curr Opin Struct Biol, 14, 43-49.  
15178685 L.Larivière, and S.Moréra (2004).
Structural evidence of a passive base-flipping mechanism for beta-glucosyltransferase.
  J Biol Chem, 279, 34715-34720.
PDB codes: 1sxp 1sxq
15273302 P.Amara, L.Serre, B.Castaing, and A.Thomas (2004).
Insights into the DNA repair process by the formamidopyrimidine-DNA glycosylase investigated by molecular dynamics.
  Protein Sci, 13, 2009-2021.  
15232006 S.Doublié, V.Bandaru, J.P.Bond, and S.S.Wallace (2004).
The crystal structure of human endonuclease VIII-like 1 (NEIL1) reveals a zincless finger motif required for glycosylase activity.
  Proc Natl Acad Sci U S A, 101, 10284-10289.
PDB code: 1tdh
14769949 V.V.Koval, N.A.Kuznetsov, D.O.Zharkov, A.A.Ishchenko, K.T.Douglas, G.A.Nevinsky, and O.S.Fedorova (2004).
Pre-steady-state kinetics shows differences in processing of various DNA lesions by Escherichia coli formamidopyrimidine-DNA glycosylase.
  Nucleic Acids Res, 32, 926-935.  
14661275 A.David, N.Bleimling, C.Beuck, J.M.Lehn, E.Weinhold, and M.P.Teulade-Fichou (2003).
DNA mismatch-specific base flipping by a bisacridine macrocycle.
  Chembiochem, 4, 1326-1331.  
14527324 G.L.Verdine, and D.P.Norman (2003).
Covalent trapping of protein-DNA complexes.
  Annu Rev Biochem, 72, 337-366.  
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
14525999 J.C.Fromme, and G.L.Verdine (2003).
DNA lesion recognition by the bacterial repair enzyme MutM.
  J Biol Chem, 278, 51543-51548.
PDB codes: 1r2y 1r2z
12505993 K.D.Corbett, and J.M.Berger (2003).
Structure of the topoisomerase VI-B subunit: implications for type II topoisomerase mechanism and evolution.
  EMBO J, 22, 151-163.
PDB codes: 1mu5 1mx0
12654914 K.Kwon, C.Cao, and J.T.Stivers (2003).
A novel zinc snap motif conveys structural stability to 3-methyladenine DNA glycosylase I.
  J Biol Chem, 278, 19442-19446.
PDB code: 1nku
14503888 M.D.Leipold, H.Workman, J.G.Muller, C.J.Burrows, and S.S.David (2003).
Recognition and removal of oxidized guanines in duplex DNA by the base excision repair enzymes hOGG1, yOGG1, and yOGG2.
  Biochemistry, 42, 11373-11381.  
12846827 M.Taranenko, A.Rykhlevskaya, M.Mtchedlidze, J.Laval, and S.Kuznetsova (2003).
Photochemical cross-linking of Escherichia coli Fpg protein to DNA duplexes containing phenyl(trifluoromethyl)diazirine groups.
  Eur J Biochem, 270, 2945-2949.  
12209008 D.T.Lesher, Y.Pommier, L.Stewart, and M.R.Redinbo (2002).
8-Oxoguanine rearranges the active site of human topoisomerase I.
  Proc Natl Acad Sci U S A, 99, 12102-12107.
PDB code: 1lpq
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.