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PDBsum entry 1ee8

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protein metals Protein-protein interface(s) links
DNA binding protein PDB id
1ee8
Jmol
Contents
Protein chains
266 a.a. *
Metals
_ZN ×2
Waters ×292
* Residue conservation analysis
PDB id:
1ee8
Name: DNA binding protein
Title: Crystal structure of mutm (fpg) protein from thermus thermop
Structure: Mutm (fpg) protein. Chain: a, b. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.90Å     R-factor:   0.214     R-free:   0.258
Authors: M.Sugahara,T.Mikawa,T.Kumasaka,M.Yamamoto,R.Kato,K.Fukuyama, S.Kuramitsu,Riken Structural Genomics/proteomics Initiative
Key ref:
M.Sugahara et al. (2000). Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile, Thermus thermophilus HB8. EMBO J, 19, 3857-3869. PubMed id: 10921868 DOI: 10.1093/emboj/19.15.3857
Date:
31-Jan-00     Release date:   31-Jan-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O50606  (FPG_THET8) -  Formamidopyrimidine-DNA glycosylase
Seq:
Struc:
267 a.a.
266 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: E.C.3.2.2.23  - DNA-formamidopyrimidine glycosylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of DNA containing ring-opened N(7)-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimide.
   Enzyme class 3: E.C.4.2.99.18  - DNA-(apurinic or apyrimidinic site) lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   6 terms 
  Biochemical function     catalytic activity     12 terms  

 

 
DOI no: 10.1093/emboj/19.15.3857 EMBO J 19:3857-3869 (2000)
PubMed id: 10921868  
 
 
Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile, Thermus thermophilus HB8.
M.Sugahara, T.Mikawa, T.Kumasaka, M.Yamamoto, R.Kato, K.Fukuyama, Y.Inoue, S.Kuramitsu.
 
  ABSTRACT  
 
protein is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidatively damaged bases (N-glycosylase activity) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity). The crystal structure of MutM from an extreme thermophile, Thermus thermophilus HB8, was determined at 1.9 A resolution with multiwavelength anomalous diffraction phasing using the intrinsic Zn(2+) ion of the zinc finger. MutM is composed of two distinct and novel domains connected by a flexible hinge. There is a large, electrostatically positive cleft lined by highly conserved residues between the domains. On the basis of the three-dimensional structure and taking account of previous biochemical experiments, we propose a DNA-binding mode and reaction mechanism for MutM. The locations of the putative catalytic residues and the two DNA-binding motifs (the zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes.
 
  Selected figure(s)  
 
Figure 5.
Figure 5 The structural basis for lesion recognition in MutM. (A) Model of recognition of GO:C-paired DNA (grey) by conserved amino acid residues (ball-and-stick) of MutM. (B) Schematic representation of the proposed lesion-recognition mechanism for the GO:C pair in dsDNA. Arg99 and Arg253 can interact with the keto groups of the GO and C base pair (blue) in both sides of dsDNA to disrupt the pairing hydrogen bonds in the model. The C8 oxo group of the GO base (red) in the DNA major groove could be pulled off by Met70 or Phe101 in the N-terminal domain. Phe101 could be inserted into the vacant site after nucleotide flipping to compensate for base stacking in the dsDNA. (C) Pairing of the oxidized bases in high- and low-efficiency MutM substrates is shown in the upper and lower rows, respectively (Hatahet et al., 1994; Tchou et al., 1994).
Figure 7.
Figure 7 Schematic representation of the reaction mechanism of MutM N-glycosylase/AP lyase. The reaction scheme is proposed on the basis of the active site architecture according to the mechanism proposed by Castaing et al. (1999). We propose that the invariant amino acid residues (Glu2, Glu5 and Lys52) in the vicinity of the primary catalytic residue Pro1, whose N-terminal amine forms a Schiff base with the C1' of damaged deoxyribose (Zharkov et al., 1997), act as the additional catalytic residues for the enzyme action and, together with their bound water molecules, form a hydrogen bond network in the active site. In this highly electrostatically positive environment, Lys52 may act as a proton donor for the depurination of the damaged base (Figure 6B). After C2' of deoxyribose has formed a Schiff base with Pro1, Glu5 could withdraw the proton of C2' via a bound water, leading to -elimination. The resulting adduct intermediate (Figure 6C) would deprotonate at C4' of the opened deoxyribose, leading to -elimination. Finally, regain of the proton by Lys52 would release the other product, 4-oxo-2-pentenal, to form the gapped dsDNA product (Bhagwat and Gerlt, 1996). The residues believed to contribute to each reaction step were deduced from the crystal structure and are shown in red.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 3857-3869) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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.  
19223326 Q.M.Zhang-Akiyama, H.Morinaga, M.Kikuchi, S.Yonekura, H.Sugiyama, K.Yamamoto, and S.Yonei (2009).
KsgA, a 16S rRNA adenine methyltransferase, has a novel DNA glycosylase/AP lyase activity to prevent mutations in Escherichia coli.
  Nucleic Acids Res, 37, 2116-2125.  
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
18635007 F.Coste, M.Ober, Y.V.Le Bihan, M.A.Izquierdo, N.Hervouet, H.Mueller, T.Carell, and B.Castaing (2008).
Bacterial base excision repair enzyme Fpg recognizes bulky N7-substituted-FapydG lesion via unproductive binding mode.
  Chem Biol, 15, 706-717.
PDB code: 3c58
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.  
17627905 V.Bandaru, X.Zhao, M.R.Newton, C.J.Burrows, and S.S.Wallace (2007).
Human endonuclease VIII-like (NEIL) proteins in the giant DNA Mimivirus.
  DNA Repair (Amst), 6, 1629-1641.  
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
16024742 N.A.Kuznetsov, V.V.Koval, D.O.Zharkov, G.A.Nevinsky, K.T.Douglas, and O.S.Fedorova (2005).
Kinetics of substrate recognition and cleavage by human 8-oxoguanine-DNA glycosylase.
  Nucleic Acids Res, 33, 3919-3931.  
15339932 A.Das, L.Rajagopalan, V.S.Mathura, S.J.Rigby, S.Mitra, and T.K.Hazra (2004).
Identification of a zinc finger domain in the human NEIL2 (Nei-like-2) protein.
  J Biol Chem, 279, 47132-47138.
PDB code: 1vzp
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
15272182 G.Golan, D.O.Zharkov, A.S.Fernandes, E.Zaika, J.H.Kycia, Z.Wawrzak, A.P.Grollman, and G.Shoham (2004).
Crystallization and preliminary crystallographic analysis of endonuclease VIII in its uncomplexed form.
  Acta Crystallogr D Biol Crystallogr, 60, 1476-1480.  
15102448 J.C.Fromme, A.Banerjee, and G.L.Verdine (2004).
DNA glycosylase recognition and catalysis.
  Curr Opin Struct Biol, 14, 43-49.  
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.  
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
14501132 S.Yoshiba, N.Nakagawa, R.Masui, T.Shibata, Y.Inoue, S.Yokoyama, and S.Kuramitsu (2003).
Overproduction, crystallization and preliminary diffraction data of ADP-ribose pyrophosphatase from Thermus thermophilus HB8.
  Acta Crystallogr D Biol Crystallogr, 59, 1840-1842.  
12056884 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.
  Biochemistry, 41, 7540-7548.  
12207707 C.A.Blindauer, M.D.Harrison, A.K.Robinson, J.A.Parkinson, P.W.Bowness, P.J.Sadler, and N.J.Robinson (2002).
Multiple bacteria encode metallothioneins and SmtA-like zinc fingers.
  Mol Microbiol, 45, 1421-1432.  
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.  
11847126 D.O.Zharkov, G.Golan, R.Gilboa, A.S.Fernandes, S.E.Gerchman, J.H.Kycia, R.A.Rieger, A.P.Grollman, and G.Shoham (2002).
Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate.
  EMBO J, 21, 789-800.
PDB codes: 1k3w 1k3x
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
12433996 I.Morland, V.Rolseth, L.Luna, T.Rognes, M.Bjørås, and E.Seeberg (2002).
Human DNA glycosylases of the bacterial Fpg/MutM superfamily: an alternative pathway for the repair of 8-oxoguanine and other oxidation products in DNA.
  Nucleic Acids Res, 30, 4926-4936.  
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
11914495 K.Pereira de Jésus, L.Serre, N.Hervouet, V.Bouckson-Castaing, C.Zelwer, and B.Castaing (2002).
Crystallization and preliminary X-ray crystallographic studies of a complex between the Lactococcus lactis Fpg DNA-repair enzyme and an abasic site containing DNA.
  Acta Crystallogr D Biol Crystallogr, 58, 679-682.  
12065399 L.Serre, K.Pereira de Jésus, S.Boiteux, C.Zelwer, and B.Castaing (2002).
Crystal structure of the Lactococcus lactis formamidopyrimidine-DNA glycosylase bound to an abasic site analogue-containing DNA.
  EMBO J, 21, 2854-2865.
PDB code: 1kfv
11813291 M.Saparbaev, O.M.Sidorkina, J.Jurado, C.V.Privezentzev, M.M.Greenberg, and J.Laval (2002).
Repair of oxidized purines and damaged pyrimidines by E. coli Fpg protein: different roles of proline 2 and lysine 57 residues.
  Environ Mol Mutagen, 39, 10-17.  
12200441 M.Takao, S.Kanno, K.Kobayashi, Q.M.Zhang, S.Yonei, G.T.van der Horst, and A.Yasui (2002).
A back-up glycosylase in Nth1 knock-out mice is a functional Nei (endonuclease VIII) homologue.
  J Biol Chem, 277, 42205-42213.  
11912217 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: 1k82
11904416 T.K.Hazra, T.Izumi, I.Boldogh, B.Imhoff, Y.W.Kow, P.Jaruga, M.Dizdaroglu, and S.Mitra (2002).
Identification and characterization of a human DNA glycosylase for repair of modified bases in oxidatively damaged DNA.
  Proc Natl Acad Sci U S A, 99, 3523-3528.  
12220492 T.Kumasaka, M.Yamamoto, E.Yamashita, H.Moriyama, and T.Ueki (2002).
Trichromatic concept optimizes MAD experiments in synchrotron X-ray crystallography.
  Structure, 10, 1205-1210.  
11238994 A.E.Vidal, I.D.Hickson, S.Boiteux, and J.P.Radicella (2001).
Mechanism of stimulation of the DNA glycosylase activity of hOGG1 by the major human AP endonuclease: bypass of the AP lyase activity step.
  Nucleic Acids Res, 29, 1285-1292.  
11580290 M.Dizdaroglu, S.M.Burgess, P.Jaruga, T.K.Hazra, H.Rodriguez, and R.S.Lloyd (2001).
Substrate specificity and excision kinetics of Escherichia coli endonuclease VIII (Nei) for modified bases in DNA damaged by free radicals.
  Biochemistry, 40, 12150-12156.  
11557810 X.Cheng, and R.J.Roberts (2001).
AdoMet-dependent methylation, DNA methyltransferases and base flipping.
  Nucleic Acids Res, 29, 3784-3795.  
11106507 O.V.Lavrukhin, and R.S.Lloyd (2000).
Involvement of phylogenetically conserved acidic amino acid residues in catalysis by an oxidative DNA damage enzyme formamidopyrimidine glycosylase.
  Biochemistry, 39, 15266-15271.  
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.