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Hydrolase/DNA PDB id
1fn7
Jmol
Contents
Protein chain
314 a.a. *
DNA/RNA
Metals
_CA
Waters ×132
* Residue conservation analysis
PDB id:
1fn7
Name: Hydrolase/DNA
Title: Coupling of damage recognition and catalysis by a human base-excision DNA repair protein
Structure: DNA (5'- d( Gp Gp Tp Ap Gp Ap Cp Cp Tp Gp Gp Ap Cp Gp C)-3'). Chain: c. Engineered: yes. DNA (5'-d( Gp Cp Gp Tp Cp Cp Ap (3Dr) p Gp Tp Cp Tp Ap Cp C)-3'). Chain: d. Engineered: yes. 8-oxoguanine DNA glycosylase 1.
Source: Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PQS)
Resolution:
2.60Å     R-factor:   0.221     R-free:   0.270
Authors: D.P.G.Norman,S.D.Bruner,G.L.Verdine
Key ref: D.P.Norman et al. (2001). Coupling of substrate recognition and catalysis by a human base-excision DNA repair protein. J Am Chem Soc, 123, 359-360. PubMed id: 11456534 DOI: 10.1021/ja003144m
Date:
21-Aug-00     Release date:   21-Apr-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O15527  (OGG1_HUMAN) -  N-glycosylase/DNA lyase
Seq:
Struc: 		345 a.a.
314 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: 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.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   5 terms 
  Biological process     metabolic process   10 terms 
  Biochemical function     catalytic activity     10 terms  

 

 
DOI no: 10.1021/ja003144m J Am Chem Soc 123:359-360 (2001)
PubMed id: 11456534  
 
 
Coupling of substrate recognition and catalysis by a human base-excision DNA repair protein.
D.P.Norman, S.D.Bruner, G.L.Verdine.
 
  ABSTRACT  
 
No abstract given.

 

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
19674107 V.S.Sidorenko, A.P.Grollman, P.Jaruga, M.Dizdaroglu, and D.O.Zharkov (2009).
Substrate specificity and excision kinetics of natural polymorphic variants and phosphomimetic mutants of human 8-oxoguanine-DNA glycosylase.
  FEBS J, 276, 5149-5162.  
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
17114185 C.T.Radom, A.Banerjee, and G.L.Verdine (2007).
Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations.
  J Biol Chem, 282, 9182-9194.
PDB codes: 2nob 2noe 2nof 2noh 2noi 2nol 2noz
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.  
17116430 T.K.Hazra, A.Das, S.Das, S.Choudhury, Y.W.Kow, and R.Roy (2007).
Oxidative DNA damage repair in mammalian cells: a new perspective.
  DNA Repair (Amst), 6, 470-480.  
17015827 A.Banerjee, and G.L.Verdine (2006).
A nucleobase lesion remodels the interaction of its normal neighbor in a DNA glycosylase complex.
  Proc Natl Acad Sci U S A, 103, 15020-15025.
PDB code: 2i5w
16549874 J.W.Hill, and M.K.Evans (2006).
Dimerization and opposite base-dependent catalytic impairment of polymorphic S326C OGG1 glycosylase.
  Nucleic Acids Res, 34, 1620-1632.  
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.  
15800616 A.Banerjee, W.Yang, M.Karplus, and G.L.Verdine (2005).
Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA.
  Nature, 434, 612-618.
PDB codes: 1yqk 1yql 1yqm 1yqr
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.  
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.  
14752045 P.A.van der Kemp, J.B.Charbonnier, M.Audebert, and S.Boiteux (2004).
Catalytic and DNA-binding properties of the human Ogg1 DNA N-glycosylase/AP lyase: biochemical exploration of H270, Q315 and F319, three amino acids of the 8-oxoguanine-binding pocket.
  Nucleic Acids Res, 32, 570-578.  
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.  
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
12592398 J.C.Fromme, S.D.Bruner, W.Yang, M.Karplus, and G.L.Verdine (2003).
Product-assisted catalysis in base-excision DNA repair.
  Nat Struct Biol, 10, 204-211.
PDB codes: 1hu0 1lwv 1lww 1lwy
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
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
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
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.