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(-) Description

Title :  VERY-SHORT-PATCH DNA REPAIR ENDONUCLEASE BOUND TO ITS REACTION PRODUCT SITE
 
Authors :  K. A. Bunting, S. M. Roe, A. Headley, T. Brown, R. Savva, L. H. Pearl
Date :  19 Feb 03  (Deposition) - 13 Mar 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,F,W
Keywords :  Hydrolase, Dna Repair, Endonuclease, Very Short Patch Repair, Dna Repai Hydrolase, Nuclease, Zinc, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. A. Bunting, S. M. Roe, A. Headley, T. Brown, R. Savva, L. H. Pearl
Crystal Structure Of The Escherichia Coli Dcm Very-Short-Patch Dna Repair Endonuclease Bound To Its Reaction Product-Site In A Dna Superhelix
Nucleic Acids Res. V. 31 1633 2003
PubMed-ID: 12626704  |  Reference-DOI: 10.1093/NAR/GKG273

(-) Compounds

Molecule 1 - DNA MISMATCH ENDONUCLEASE
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28
    Expression System StrainB834 (DE3)
    Expression System Taxid562
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymVERY SHORT PATCH REPAIR PROTEIN, VSR MISMATCH ENDONUCLEASE, V.ECOKDCM, VSR, B1960
 
Molecule 2 - 5'-D(*TP*AP*GP*GP*CP*5CM*TP*GP*GP*AP*TP*CP)-3'
    ChainsF, W
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit AFW

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
15CM2Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:66 , HIS A:71 , CYS A:73 , CYS A:117BINDING SITE FOR RESIDUE ZN A 200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ODG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ODG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ODG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ODG)

(-) Exons   (0, 0)

(no "Exon" information available for 1ODG)

(-) 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:134
 aligned with VSR_ECOLI | P09184 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:134
                                    32        42        52        62        72        82        92       102       112       122       132       142       152    
            VSR_ECOLI    23 AIEKRLASLLTGQGLAFRVQDASLPGRPDFVVDEYRCVIFTHGCFWHHHHCYLFKVPATRTEFWLEKIGKNVERDRRDISRLQELGWRVLIVWECALRGREKLTDEALTERLEEWICGEGASAQIDTQGIHLLA 156
               SCOP domains d1odga_ A: Very short patch repair (VSR) endonuclease                                                                                  SCOP domains
               CATH domains 1odgA00 A:23-156 VSR Endonuclease                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..eee..........eee....eeee...................hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhh......hhhhhhhhhhhhhh.....eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1odg A  23 AIEKRLASLLTGQGLAFRVQDASLPGRPDFVVDEYRCVIFTHGCFWHHHHCYLFKVPATRTEFWLEKIGKNVERDRRDISRLQELGWRVLIVWECALRGREKLTDEALTERLEEWICGEGASAQIDTQGIHLLA 156
                                    32        42        52        62        72        82        92       102       112       122       132       142       152    

Chain F from PDB  Type:DNA  Length:12
                                            
                 1odg F   1 TAGGCcTGGATC  12
                                 |  10  
                                 6-5CM  

Chain W from PDB  Type:DNA  Length:12
                                            
                 1odg W   1 TAGGCcTGGATC  12
                                 |  10  
                                 6-5CM  

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1ODG)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (VSR_ECOLI | P09184)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043765    T/G mismatch-specific endonuclease activity    Catalysis of the repair of T/G mismatches arising from deamination of 5-methylcytosine in DNA by nicking double-stranded DNA within the sequence CT(AT)GN or NT(AT)GG next to the mismatched thymidine residue. The incision is mismatch-dependent and strand-specific, in favor of the G-containing strand. The incision serves as a starting point for subsequent excision repair by DNA polymerase I, which excises thymidine and reinserts cytidine.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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: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:0006298    mismatch repair    A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.
    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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        VSR_ECOLI | P091841cw0 1vsr

(-) Related Entries Specified in the PDB File

1cw0 CRYSTAL STRUCTURE ANALYSIS OF VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE IN COMPLEX WITH A DUPLEX DEOXYRIBONUCLEIC ACID
1vsr VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE FROM ESCHERICHIA COLI