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(-) Description

Title :  CRYSTAL STRUCTURE OF METHANOCALDOCOCCUS JANNASCHII 8-OXOGUANINE GLYCOSYLASE/LYASE IN COMPLEX WITH 15MER DNA CONTAINING 8-OXOGUANINE
 
Authors :  F. Faucher, S. Doublie
Date :  12 Nov 09  (Deposition) - 02 Feb 10  (Release) - 16 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,C,D,E,F,G,H,I,J,K,L  (1x)
Biol. Unit 2:  A,E,F  (1x)
Biol. Unit 3:  B,G,H  (1x)
Biol. Unit 4:  C,I,J  (1x)
Biol. Unit 5:  D,K,L  (1x)
Keywords :  Protein-Dna Complex, Ogg, Helix-Hairpin-Helix, Glycosylase, 8-Oxoguanine, 8-Oxog, Dna Repair, Dna Damage, Glycosidase, Multifunctional Enzyme, Nuclease, Hydrolase, Lyase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Faucher, S. S. Wallace, S. Doublie
The C-Terminal Lysine Of Ogg2 Dna Glycosylases Is A Major Molecular Determinant For Guanine/8-Oxoguanine Distinction.
J. Mol. Biol. V. 397 46 2010
PubMed-ID: 20083120  |  Reference-DOI: 10.1016/J.JMB.2010.01.024

(-) Compounds

Molecule 1 - N-GLYCOSYLASE/DNA LYASE
    Chains: A, B, C, D
    EC Number: 3.2.2.-, 4.2.99.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-22
    Expression System Strain: ER2566(FPG-)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: MJAOGG
    Gene: 1451601, MJ0724, OGG
    Mutation: YES
    Organism Common: METHANOCOCCUS JANNASCHII
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Synonym: 8-OXOGUANINE DNA GLYCOSYLASE, DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE, AP LYASE
 
Molecule 2 - 5'-D(*AP*CP*GP*TP*CP*CP*AP*(8OG) P*GP*TP*CP*TP*AP*CP*C)-3'
    Chains: E, G, I, K
    Engineered: YES
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS.
    Synthetic: YES
 
Molecule 3 - 5'- D(*TP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'
    Chains: F, H, J, L
    Engineered: YES
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): ABCDEFGHIJKL
Biological Unit 2 (1x): A   EF      
Biological Unit 3 (1x):  B    GH    
Biological Unit 4 (1x):   C     IJ  
Biological Unit 5 (1x):    D      KL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
18OG4Mod. Nucleotide8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
2NA4Ligand/IonSODIUM ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
18OG4Mod. Nucleotide8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
18OG1Mod. Nucleotide8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
2NA-1Ligand/IonSODIUM ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
18OG1Mod. Nucleotide8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
2NA-1Ligand/IonSODIUM ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
18OG1Mod. Nucleotide8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
2NA-1Ligand/IonSODIUM ION
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
18OG1Mod. Nucleotide8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
2NA-1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:120 , ILE A:123 , ILE A:126 , DC E:26BINDING SITE FOR RESIDUE NA A 208
2AC2SOFTWAREVAL B:120 , ILE B:123 , ILE B:126 , DC G:26BINDING SITE FOR RESIDUE NA B 208
3AC3SOFTWAREVAL C:120 , ILE C:123 , ILE C:126 , DC I:26BINDING SITE FOR RESIDUE NA C 208
4AC4SOFTWAREVAL D:120 , ILE D:123 , ILE D:126 , DC K:26BINDING SITE FOR RESIDUE NA D 208

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KNT)

(-) Sequences/Alignments

Asymmetric 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:207
 aligned with OGG1_METJA | Q58134 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       
           OGG1_METJA     1 MMLIKKIEELKNSEIKDIIDKRIQEFKSFKNKSNEEWFKELCFCILTANFTAEGGIRIQKEIGDGFLTLPREELEEKLKNLGHRFYRKRAEYIVLARRFKNIKDIVESFENEKVAREFLVRNIKGIGYKEASHFLRNVGYDDVAIIDRHILRELYENNYIDEIPKTLSRRKYLEIENILRDIGEEVNLKLSELDLYIWYLRTGKVLK 207
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhh........hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3knt A   1 MMLIKKIEELKNSEIKDIIDKRIQEFKSFKNKSNEEWFKELCFCILTANFTAEGGIRIQKEIGDGFLTLPREELEEKLKNLGHRFYRKRAEYIVLARRFKNIKDIVESFENEKVAREFLVRNIKGIGYQEASHFLRNVGYDDVAIIDRHILRELYENNYIDEIPKTLSRRKYLEIENILRDIGEEVNLKLSELDLYIWYLRTGKVLK 207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       


Chain B from PDB  Type:PROTEIN  Length:207
 aligned with OGG1_METJA | Q58134 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       
           OGG1_METJA     1 MMLIKKIEELKNSEIKDIIDKRIQEFKSFKNKSNEEWFKELCFCILTANFTAEGGIRIQKEIGDGFLTLPREELEEKLKNLGHRFYRKRAEYIVLARRFKNIKDIVESFENEKVAREFLVRNIKGIGYKEASHFLRNVGYDDVAIIDRHILRELYENNYIDEIPKTLSRRKYLEIENILRDIGEEVNLKLSELDLYIWYLRTGKVLK 207
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhhh........hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3knt B   1 MMLIKKIEELKNSEIKDIIDKRIQEFKSFKNKSNEEWFKELCFCILTANFTAEGGIRIQKEIGDGFLTLPREELEEKLKNLGHRFYRKRAEYIVLARRFKNIKDIVESFENEKVAREFLVRNIKGIGYQEASHFLRNVGYDDVAIIDRHILRELYENNYIDEIPKTLSRRKYLEIENILRDIGEEVNLKLSELDLYIWYLRTGKVLK 207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       


Chain C from PDB  Type:PROTEIN  Length:205
 aligned with OGG1_METJA | Q58134 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:205
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202     
           OGG1_METJA     3 LIKKIEELKNSEIKDIIDKRIQEFKSFKNKSNEEWFKELCFCILTANFTAEGGIRIQKEIGDGFLTLPREELEEKLKNLGHRFYRKRAEYIVLARRFKNIKDIVESFENEKVAREFLVRNIKGIGYKEASHFLRNVGYDDVAIIDRHILRELYENNYIDEIPKTLSRRKYLEIENILRDIGEEVNLKLSELDLYIWYLRTGKVLK 207
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhh........hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3knt C   3 LIKKIEELKNSEIKDIIDKRIQEFKSFKNKSNEEWFKELCFCILTANFTAEGGIRIQKEIGDGFLTLPREELEEKLKNLGHRFYRKRAEYIVLARRFKNIKDIVESFENEKVAREFLVRNIKGIGYQEASHFLRNVGYDDVAIIDRHILRELYENNYIDEIPKTLSRRKYLEIENILRDIGEEVNLKLSELDLYIWYLRTGKVLK 207
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202     


Chain D from PDB  Type:PROTEIN  Length:206
 aligned with OGG1_METJA | Q58134 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:206
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201      
           OGG1_METJA     2 MLIKKIEELKNSEIKDIIDKRIQEFKSFKNKSNEEWFKELCFCILTANFTAEGGIRIQKEIGDGFLTLPREELEEKLKNLGHRFYRKRAEYIVLARRFKNIKDIVESFENEKVAREFLVRNIKGIGYKEASHFLRNVGYDDVAIIDRHILRELYENNYIDEIPKTLSRRKYLEIENILRDIGEEVNLKLSELDLYIWYLRTGKVLK 207
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh........hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3knt D   2 MLIKKIEELKNSEIKDIIDKRIQEFKSFKNKSNEEWFKELCFCILTANFTAEGGIRIQKEIGDGFLTLPREELEEKLKNLGHRFYRKRAEYIVLARRFKNIKDIVESFENEKVAREFLVRNIKGIGYQEASHFLRNVGYDDVAIIDRHILRELYENNYIDEIPKTLSRRKYLEIENILRDIGEEVNLKLSELDLYIWYLRTGKVLK 207
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201      


Chain E from PDB  Type:DNA  Length:15
                                               
                 3knt E  16 ACGTCCAgGTCTACC  30
                                   |25     
                                  23-8OG   


Chain F from PDB  Type:DNA  Length:15
                                               
                 3knt F   1 TGGTAGACCTGGACG  15
                                    10     


Chain G from PDB  Type:DNA  Length:13
                                             
                 3knt G  16 ACGTCCAgGTCTA  28
                                   |25   
                                  23-8OG 


Chain H from PDB  Type:DNA  Length:13
                                             
                 3knt H   3 GTAGACCTGGACG  15
                                    12   


Chain I from PDB  Type:DNA  Length:14
                                              
                 3knt I  16 ACGTCCAgGTCTAC  29
                                   |25    
                                  23-8OG  


Chain J from PDB  Type:DNA  Length:13
                                             
                 3knt J   3 GTAGACCTGGACG  15
                                    12   


Chain K from PDB  Type:DNA  Length:15
                                               
                 3knt K  16 ACGTCCAgGTCTACC  30
                                   |25     
                                  23-8OG   


Chain L from PDB  Type:DNA  Length:15
                                               
                 3knt L   1 TGGTAGACCTGGACG  15
                                    10
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 3KNT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (OGG1_METJA | Q58134)
molecular function
    GO:0003906    DNA-(apurinic or apyrimidinic site) lyase activity    Catalysis of the cleavage of the C-O-P bond 3' to the apurinic or apyrimidinic site in DNA by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.
    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:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0016799    hydrolase activity, hydrolyzing N-glycosyl compounds    Catalysis of the hydrolysis of any N-glycosyl bond.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
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:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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        OGG1_METJA | Q58134: 3fhf

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