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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE IN COMPLEX WITH A DUPLEX DNA
 
Authors :  S. E. Tsutakawa, H. Jingami, K. Morikawa
Date :  25 Aug 99  (Deposition) - 12 Dec 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,M,N,O
Keywords :  Protein-Dna Complex, Mismatch, Intercalation, Zinc, Hydrolase/Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. E. Tsutakawa, H. Jingami, K. Morikawa
Recognition Of A Tg Mismatch: The Crystal Structure Of Very Short Patch Repair Endonuclease In Complex With A Dna Duplex.
Cell(Cambridge, Mass. ) V. 99 615 1999
PubMed-ID: 10612397  |  Reference-DOI: 10.1016/S0092-8674(00)81550-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*AP*CP*GP*TP*AP*CP*CP*TP*GP*GP*CP*T)- 3')
    ChainsM
    EngineeredYES
    SyntheticYES
 
Molecule 2 - DNA (5'-D(*AP*GP*C)-3')
    ChainsN
    EngineeredYES
    SyntheticYES
 
Molecule 3 - DNA (5'-D(P*TP*AP*GP*GP*TP*AP*CP*GP*T)-3')
    ChainsO
    EngineeredYES
    SyntheticYES
 
Molecule 4 - PROTEIN (DNA MISMATCH ENDONUCLEASE)
    ChainsA
    EC Number3.1.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymVSR ENDONUCLEASE, PATCH REPAIR PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit AMNO

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:66 , HIS A:71 , CYS A:73 , CYS A:117BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWAREARG A:49 , ASP A:51 , HOH A:496 , HOH A:498 , HOH A:596 , DC N:353 , DT O:354BINDING SITE FOR RESIDUE MG N 202
3AC3SOFTWAREASP A:51 , THR A:63 , HOH A:494 , DT O:354 , HOH O:495BINDING SITE FOR RESIDUE MG A 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1CW0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1CW0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CW0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1CW0)

(-) Exons   (0, 0)

(no "Exon" information available for 1CW0)

(-) 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:155
 aligned with VSR_ECOLI | P09184 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:155
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151     
            VSR_ECOLI     2 ADVHDKATRSKNMRAIATRDTAIEKRLASLLTGQGLAFRVQDASLPGRPDFVVDEYRCVIFTHGCFWHHHHCYLFKVPATRTEFWLEKIGKNVERDRRDISRLQELGWRVLIVWECALRGREKLTDEALTERLEEWICGEGASAQIDTQGIHLLA 156
               SCOP domains d1cw0a_ A: Very short patch repair (VSR) endonuclease                                                                                                       SCOP domains
               CATH domains 1cw0A00 A:2-156 VSR Endonuclease                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh....hhhhhhhhhhhhhh....ee..........eeehhh.eeeeee.................hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeehhhhh.....hhhhhhhhhhhhhhh....eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cw0 A   2 ADVHDKATRSKNMRAIATRDTAIEKRLASLLTGQGLAFRVQDASLPGRPDFVVDEYRCVIFTHGCFWHHHHCYLFKVPATRTEFWLEKIGKNVERDRRDISRLQELGWRVLIVWECALRGREKLTDEALTERLEEWICGEGASAQIDTQGIHLLA 156
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151     

Chain M from PDB  Type:DNA  Length:12
                                            
                 1cw0 M 301 ACGTACCTGGCT 312
                                   310  

Chain N from PDB  Type:DNA  Length:3
                                   
                 1cw0 N 351 AGC 353

Chain O from PDB  Type:DNA  Length:9
                                         
                 1cw0 O 354 TAGGTACGT 362

   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  (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 1CW0)

(-) 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 | P091841odg 1vsr

(-) Related Entries Specified in the PDB File

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