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(-) Description

Title :  CRYSTAL STRUCTURE OF TM1821, THE 8-OXOGUANINE DNA GLYCOSYLASE OF THERMOTOGA MARITIMA
 
Authors :  D. R. Cooper, A. Roy, Z. S. Derewenda, Integrated Center For Structu Function Innovation (Isfi)
Date :  14 May 10  (Deposition) - 06 Apr 11  (Release) - 06 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Structural Genomics, Isfi, Dna Repair, 8-Oxoguanine, Base Excision Repair, Psi-2, Protein Structure Initiative, Integrated Center For Structure And Function Innovation, Hydrolase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. R. Cooper, A. Roy, Z. S. Derewenda
Crystal Structure Of Tm1821, The 8-Oxoguanine Dna Glycosylase Of Thermotoga Maritima
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE N-GLYCOSYLASE/DNA LYASE
    Chains: A, B, C
    EC Number: 3.2.2.-, 4.2.99.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: OGG, TM1821, TM_1821
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: 8-OXOGUANINE DNA GLYCOSYLASE, DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE, AP LYASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1NA3Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:119 , VAL A:120 , ALA A:123 , ILE A:126 , HOH A:277 , HOH A:399BINDING SITE FOR RESIDUE NA A 208
2AC2SOFTWARELEU B:119 , VAL B:120 , ALA B:123 , ILE B:126 , HOH B:267 , HOH B:298BINDING SITE FOR RESIDUE NA B 208
3AC3SOFTWARELEU C:119 , VAL C:120 , ALA C:123 , ILE C:126 , HOH C:334 , HOH C:415BINDING SITE FOR RESIDUE NA C 208

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N0U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3N0U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N0U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3N0U)

(-) Exons   (0, 0)

(no "Exon" information available for 3N0U)

(-) 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:209
 aligned with OGG1_THEMA | Q9X2E1 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:209
                              1                                                                                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198         
           OGG1_THEMA     - --MEELLKELERIREEAKPLVEQRFEEFKRLGEEGTEEDLFCELSFCVLTANWSAEGGIRAQKEIGKGFVHLPLEELAEKLREVGHRYPQKRAEFIVENRKLLGKLKNLVKGDPFQSREFLVRNAKGIGWKEASHFLRNTGVEDLAILDKHVLRLMKRHGLIQEIPKGWSKKRYLYVEEILRKVAEAFGESPGKFDLYLWYLVKGKVDK 207
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n0u A  -1 HHMEELLKELERIREEAKPLVEQRFEEFKRLGEEGTEEDLFCELSFCVLTANWSAEGGIRAQKEIGKGFVHLPLEELAEKLREVGHRYPQKRAEFIVENRKLLGKLKNLVKGDPFQSREFLVRNAKGIGWKEASHFLRNTGVEDLAILDKHVLRLMKRHGLIQEIPKGWSKKRYLYVEEILRKVAEAFGESPGKFDLYLWYLVKGKVDK 207
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198         


Chain B from PDB  Type:PROTEIN  Length:209
 aligned with OGG1_THEMA | Q9X2E1 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:209
                              1                                                                                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198         
           OGG1_THEMA     - --MEELLKELERIREEAKPLVEQRFEEFKRLGEEGTEEDLFCELSFCVLTANWSAEGGIRAQKEIGKGFVHLPLEELAEKLREVGHRYPQKRAEFIVENRKLLGKLKNLVKGDPFQSREFLVRNAKGIGWKEASHFLRNTGVEDLAILDKHVLRLMKRHGLIQEIPKGWSKKRYLYVEEILRKVAEAFGESPGKFDLYLWYLVKGKVDK 207
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n0u B  -1 HHMEELLKELERIREEAKPLVEQRFEEFKRLGEEGTEEDLFCELSFCVLTANWSAEGGIRAQKEIGKGFVHLPLEELAEKLREVGHRYPQKRAEFIVENRKLLGKLKNLVKGDPFQSREFLVRNAKGIGWKEASHFLRNTGVEDLAILDKHVLRLMKRHGLIQEIPKGWSKKRYLYVEEILRKVAEAFGESPGKFDLYLWYLVKGKVDK 207
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198         


Chain C from PDB  Type:PROTEIN  Length:208
 aligned with OGG1_THEMA | Q9X2E1 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:208
                             1                                                                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199        
           OGG1_THEMA     - -MEELLKELERIREEAKPLVEQRFEEFKRLGEEGTEEDLFCELSFCVLTANWSAEGGIRAQKEIGKGFVHLPLEELAEKLREVGHRYPQKRAEFIVENRKLLGKLKNLVKGDPFQSREFLVRNAKGIGWKEASHFLRNTGVEDLAILDKHVLRLMKRHGLIQEIPKGWSKKRYLYVEEILRKVAEAFGESPGKFDLYLWYLVKGKVDK 207
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------HhH-GPD-3n0uC01 C:65-183                                                                                               ------------------------ Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------HhH-GPD-3n0uC02 C:65-183                                                                                               ------------------------ Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------HhH-GPD-3n0uC03 C:65-183                                                                                               ------------------------ Pfam domains (3)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n0u C   0 HMEELLKELERIREEAKPLVEQRFEEFKRLGEEGTEEDLFCELSFCVLTANWSAEGGIRAQKEIGKGFVHLPLEELAEKLREVGHRYPQKRAEFIVENRKLLGKLKNLVKGDPFQSREFLVRNAKGIGWKEASHFLRNTGVEDLAILDKHVLRLMKRHGLIQEIPKGWSKKRYLYVEEILRKVAEAFGESPGKFDLYLWYLVKGKVDK 207
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199
   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 3N0U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N0U)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: HHH (112)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (OGG1_THEMA | Q9X2E1)
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.
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.

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