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PDBsum entry 1n3c
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protein dna_rna metals links
Hydrolase, lyase/DNA PDB id
1n3c

 

 

 

 

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Contents
Protein chain
314 a.a. *
DNA/RNA
Metals
_CA
Waters ×165
* Residue conservation analysis
PDB id:
1n3c
Name: Hydrolase, lyase/DNA
Title: Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase
Structure: DNA complement strand. Chain: b. Engineered: yes. 8-oxog-containing DNA. Chain: c. Engineered: yes. N-glycosylase/DNA lyase. Chain: a. Fragment: 3.2.2.-, 4.2.99.18.
Source: Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Gene: ogg1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Trimer (from PQS)
Resolution:
2.70Å     R-factor:   0.225     R-free:   0.273
Authors: D.P.Norman,S.J.Chung,G.L.Verdine
Key ref:
D.P.Norman et al. (2003). Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase. Biochemistry, 42, 1564-1572. PubMed id: 12578369 DOI: 10.1021/bi026823d
Date:
25-Oct-02     Release date:   04-Mar-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O15527  (OGG1_HUMAN) -  N-glycosylase/DNA lyase from Homo sapiens
Seq:
Struc: 		345 a.a.
314 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

DNA/RNA chains
  G-G-T-A-G-A-C-C-T-G-G-A-C-G-C 15 bases
  G-C-G-T-C-C-A-8OG-G-T-C-T-A-C-C 15 bases

 Enzyme reactions 
   Enzyme class 1: E.C.3.2.2.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
   Enzyme class 2: E.C.4.2.99.18  - DNA-(apurinic or apyrimidinic site) lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)- 2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3- dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-phospho- 2'-deoxyribonucleoside-DNA + H+
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.

 

 
DOI no: 10.1021/bi026823d Biochemistry 42:1564-1572 (2003)
PubMed id: 12578369  
 
 
Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase.
D.P.Norman, S.J.Chung, G.L.Verdine.
 
  ABSTRACT  
 
Members of the HhH-GPD superfamily of DNA glycosylases are responsible for the recognition and removal of damaged nucleobases from DNA. The hallmark of these proteins is a motif comprising a helix-hairpin-helix followed by a Gly/Pro-rich loop and terminating in an invariant, catalytically essential aspartic acid residue. In this study, we have probed the role of this Asp in human 8-oxoguanine DNA glycosylase (hOgg1) by mutating it to Asn (D268N), Glu (D268E), and Gln (D268Q). We show that this aspartate plays a dual role, acting both as an N-terminal alpha-helix cap and as a critical residue for catalysis of both base excision and DNA strand cleavage by hOgg1. Mutation of this residue to asparagine, another helix-capping residue, preserves stability of the protein while drastically reducing enzymatic activity. A crystal structure of this mutant is the first to reveal the active site nucleophile Lys249 in the presence of lesion-containing DNA; this structure offers a tantalizing suggestion that base excision may occur by cleavage of the glycosidic bond and then attachment of Lys249. Mutation of the aspartic acid to glutamine and glutamic acid destabilizes the protein fold to a significant extent but, surprisingly, preserves catalytic activity. Crystal structures of these mutants complexed with an unreactive abasic site in DNA reveal these residues to adopt a sterically disfavored helix-capping conformation.
 

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
19537786 P.C.Anderson, and V.Daggett (2009).
The R46Q, R131Q and R154H polymorphs of human DNA glycosylase/beta-lyase hOgg1 severely distort the active site and DNA recognition site but do not cause unfolding.
  J Am Chem Soc, 131, 9506-9515.  
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.  
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
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
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
16469697 M.Gehring, J.H.Huh, T.F.Hsieh, J.Penterman, Y.Choi, J.J.Harada, R.B.Goldberg, and R.L.Fischer (2006).
DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation.
  Cell, 124, 495-506.  
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
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 1xqu
15102448 J.C.Fromme, A.Banerjee, and G.L.Verdine (2004).
DNA glycosylase recognition and catalysis.
  Curr Opin Struct Biol, 14, 43-49.  
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.  
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.  
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
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
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.

 

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