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(-) Description

Title :  STRUCTURE OF TOPOISOMERASE DOMAIN OF TOPOISOMERASE V PROTEIN
 
Authors :  R. Rajan, B. Taneja, A. Mondragon
Date :  16 Mar 10  (Deposition) - 04 Aug 10  (Release) - 04 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Topoisomerase V, Type Ic Topoisomerase, Isomerase, Minimal Catalytic Fragment Of Topoisomerase V (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Rajan, B. Taneja, A. Mondragon
Structures Of Minimal Catalytic Fragments Of Topoisomerase Reveals Conformational Changes Relevant For Dna Binding.
Structure V. 18 829 2010
PubMed-ID: 20637419  |  Reference-DOI: 10.1016/J.STR.2010.03.006

(-) Compounds

Molecule 1 - TOPOISOMERASE V
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21 ROSETTA (DE3)
    Expression System Taxid562
    Expression System VectorPET15B
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL 31KDA FRAGMENT (TOPO-31)
    GeneMK1436, TOP5, TOPOISOMERASE V
    Organism ScientificMETHANOPYRUS KANDLERI
    Organism Taxid190192
    StrainAV19

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3M7G)

(-) Sites  (0, 0)

(no "Site" information available for 3M7G)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M7G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3M7G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M7G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3M7G)

(-) Exons   (0, 0)

(no "Exon" information available for 3M7G)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:267
 aligned with Q977W1_9EURY | Q977W1 from UniProtKB/TrEMBL  Length:984

    Alignment length:267
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       
         Q977W1_9EURY     3 LVYDAEFVGSEREFEEERETFLKGVKAYDGVLATRYLMERSSSAKNDEELLELHQNFILLTGSYACSIDPTEDRYQNVIVRGVNFDERVQRLSTGGSPARYAIVYRRGWRAIAKALDIDEEDVPAIEVRAVKRNPLQPALYRILVRYGRVDLMPVTVDEVPPEMAGEFERLIERYDVPIDEKEERILEILRENPWTPHDEIARRLGLSVSEVEGEKDPESSGIYSLWSRVVVNIEYDERTAKRHVKRRDRLLEELYEHLEELSERYL 269
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee..eehhhhhhh.....hhhhhhhh..hhhhhhhhhh..hhhhh.............hhhhhhhhhhh........hhhhhhhhhh..hhhhhhh.....hhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhh.......hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m7g A   3 LVYDAEFVGSEREFEEERETFLKGVKAYDGVLATRYLMERSSSAKNDEELLELHQNFILLTGSYACSIDPTEDRYQNVIVRGVNFDERVQRLSTGGSPARYAIVYRRGWRAIAKALDIDEEDVPAIEVRAVKRNPLQPALYRILVRYGRVDLMPVTVDEVPPEMAGEFERLIERYDVPIDEKEERILEILRENPWTPHDEIARRLGLSVSEVEGEKDPESSGIYSLWSRVVVNIEYDERTAKRHVKRRDRLLEELYEHLEELSERYL 269
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       

   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 3M7G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M7G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3M7G)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q977W1_9EURY | Q977W1)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q977W1_9EURY | Q977W12csb 2csd 3m6k 3m6z 3m7d 5hm5

(-) Related Entries Specified in the PDB File

3m6k STRUCTURE OF THE N-TERMINAL 44 KDA FRAGMENT OF TOPOISOMERASE V IN THE PRESENCE OF GUANIDIUM HYDROCHLORIDE
3m6z STRUCTURE OF THE N-TERMINAL 44 KDA FRAGMENT OF TOPOISOMERASE V IN THE PRESENCE OF GUANIDIUM HYDROCHLORIDE
3m7d STRUCTURE OF THE N-TERMINAL 44 KDA FRAGMENT OF TOPOISOMERASE V IN THE PRESENCE OF DIOXANE.