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(-) Description

Title :  CRYSTAL STRUCTURE OF CLOSTRIDIUM ACETOBUTYLICUM 8-OXOGUANINE GLYCOSYLASE/LYASE IN COMPLEX WITH DSDNA CONTAINING CYTOSINE OPPOSITE TO 8-OXOG
 
Authors :  F. Faucher, S. Doublie
Date :  25 Jun 09  (Deposition) - 29 Sep 09  (Release) - 03 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Ogg, Cacogg, Dna, 8-Oxog, 8Oxog, Glycosylase, Cytosine, Hydrolase, Lyase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Faucher, S. S. Wallace, S. Doublie
Structural Basis For The Lack Of Opposite Base Specificity Of Clostridium Acetobutylicum 8-Oxoguanine Dna Glycosylase.
Dna Repair V. 8 1283 2009
PubMed-ID: 19747886  |  Reference-DOI: 10.1016/J.DNAREP.2009.08.002
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 8-OXOGUANINE-DNA-GLYCOSYLASE
    ChainsA
    EC Number3.2.2.-, 4.2.99.18
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTYB2
    Expression System StrainER2566(FPG-)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneCAC2707, CA_C2707
    MutationYES
    Organism ScientificCLOSTRIDIUM ACETOBUTYLICUM
    Organism Taxid1488
 
Molecule 2 - 5'-D(*AP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)- 3'
    ChainsB
    EngineeredYES
    Other DetailsTHIS SEQUENCE OCCURS NATURALLY.
    SyntheticYES
 
Molecule 3 - 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*A)-3'
    ChainsC
    EngineeredYES
    Other DetailsTHIS SEQUENCE OCCURS NATURALLY.
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
18OG1Mod. Nucleotide8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
2EDO5Ligand/Ion1,2-ETHANEDIOL
3NA1Ligand/IonSODIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:50 , VAL A:51 , ASN A:65 , LEU A:148 , GLU A:149BINDING SITE FOR RESIDUE EDO A 291
2AC2SOFTWAREPHE A:48 , ASP A:114 , PRO A:115 , LYS A:202 , EDO A:293 , HOH A:384BINDING SITE FOR RESIDUE EDO A 292
3AC3SOFTWAREVAL A:74 , TYR A:78 , ARG A:112 , EDO A:292 , HOH A:531 , HOH A:550BINDING SITE FOR RESIDUE EDO A 293
4AC4SOFTWAREGLU A:142 , ILE A:154 , TYR A:155 , LYS A:269 , HOH A:304 , HOH A:361 , HOH A:435BINDING SITE FOR RESIDUE EDO A 294
5AC5SOFTWAREGLU A:22 , LEU A:23 , LYS A:24 , LYS A:56BINDING SITE FOR RESIDUE EDO A 295
6AC6SOFTWARELYS A:214 , PHE A:216 , VAL A:219 , HOH A:389 , DC B:22 , HOH B:53BINDING SITE FOR RESIDUE NA A 296

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3I0W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3I0W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3I0W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3I0W)

(-) Exons   (0, 0)

(no "Exon" information available for 3I0W)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:290
 aligned with Q97FM4_CLOAB | Q97FM4 from UniProtKB/TrEMBL  Length:292

    Alignment length:290
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
         Q97FM4_CLOAB     1 MDFDMIEEKKDSVIVRNVENFELKDIFDCGQCFRWHRQENGNYIGIAFEKVVEVQKIGEDVVIYNINEEEFKNVWSEYFDLYRDYGEIKKELSRDPLLKKSVDFGEGIRILRQDPFEILLSFIISANNRIPMIKKCINNISEKAGKKLEYKGKIYYAFPTVDKLHEFTEKDFEECTAGFRAKYLKDTVDRIYNGELNLEYIKSLNDNECHEELKKFMGVGPKVADCIMLFSMQKYSAFPVDTWVKKAMMSLYVAPDVSLKKIRDFGREKFGSLSGFAQQYLFYYARENNI 290
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...eeeee.....hhhhhhh......eee.....eeeee..eeeeeeee..eeeee..hhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhh........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.eeee..eeee...hhhhhh..hhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.......hhhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i0w A   1 MDFDMIEEKKDSVIVRNVENFELKDIFDCGQCFRWHRQENGNYIGIAFEKVVEVQKIGEDVVIYNINEEEFKNVWSEYFDLYRDYGEIKKELSRDPLLKKSVDFGEGIRILRQDPFEILLSFIISANNRIPMIKKCINNISEKAGKKLEYKGKIYYAFPTVDKLHEFTEKDFEECTAGFRAKYLKDTVDRIYNGELNLEYIKSLNDNECHEELKKFMGVGPQVADCIMLFSMQKYSAFPVDTWVKKAMMSLYVAPDVSLKKIRDFGREKFGSLSGFAQQYLFYYARENNI 290
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290

Chain B from PDB  Type:DNA  Length:13
                                             
                 3i0w B  14 ATCCAgGTCTACC  26
                                 |  23   
                                19-8OG   

Chain C from PDB  Type:DNA  Length:12
                                            
                 3i0w C   2 GGTAGACCTGGA  13
                                    11  

   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3I0W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3I0W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3I0W)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q97FM4_CLOAB | Q97FM4)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0008534    oxidized purine nucleobase lesion DNA N-glycosylase activity    Catalysis of the removal of oxidized purine bases by cleaving the N-C1' glycosidic bond between the oxidized purine and the deoxyribose sugar. The reaction involves the formation of a covalent enzyme-substrate intermediate. Release of the enzyme and free base by a beta-elimination or a beta, gamma-elimination mechanism results in the cleavage of the DNA backbone 3' of the apurinic (AP) site.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006284    base-excision repair    In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
    GO:0006289    nucleotide-excision repair    A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).

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