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(-)Asym./Biol. Unit
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(-) Description

Title :  CRYSTAL STRUCTURE OF AN N-TERMINAL 44 KDA FRAGMENT OF TOPOISOMERASE V IN THE PRESENCE OF DIOXANE
 
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 :  1.81
Chains :  Asym./Biol. Unit :  A
Keywords :  Helix-Hairpin-Helix, Topoisomerase, Conformational Change, Isomerase (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
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21 ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL 44 KDA FRAGMENT (TOPO-44)
    Gene: MK1436, TOP5, TOPOISOMERASE V
    Organism Scientific: METHANOPYRUS KANDLERI
    Organism Taxid: 190192
    Strain: AV19

 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 3M7D)

(-) Sites  (0, 0)

(no "Site" information available for 3M7D)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:314 -A:338

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3M7D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M7D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3M7D)

(-) Exons   (0, 0)

(no "Exon" information available for 3M7D)

(-) 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:376
 aligned with Q977W1_9EURY | Q977W1 from UniProtKB/TrEMBL  Length:984

    Alignment length:377
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       
         Q977W1_9EURY     4 VYDAEFVGSEREFEEERETFLKGVKAYDGVLATRYLMERSSSAKNDEELLELHQNFILLTGSYACSIDPTEDRYQNVIVRGVNFDERVQRLSTGGSPARYAIVYRRGWRAIAKALDIDEEDVPAIEVRAVKRNPLQPALYRILVRYGRVDLMPVTVDEVPPEMAGEFERLIERYDVPIDEKEERILEILRENPWTPHDEIARRLGLSVSEVEGEKDPESSGIYSLWSRVVVNIEYDERTAKRHVKRRDRLLEELYEHLEELSERYLRHPLTRRWIVEHKRDIMRRYLEQRIVECALKLQDRYGIREDVALCLARAFDGSISMIATTPYRTLKDVCPDLTLEEAKSVNRTLATLIDEHGLSPDAADELIEHFESIAGI 380
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....-hhhhhhhhhhhhhhhhhhhhh.......eeeeee..eehhhhhhh.....hhhhhhhh...hhhhhhhhh....................hhhhhhhhhhh........hhhhhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhh.......hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m7d A   4 VYDAEFVGSEREFEEERETFLKGVKAYDGVLATRYLMERSSSAK-DEELLELHQNFILLTGSYACSIDPTEDRYQNVIVRGVNFDERVQRLSTGGSPARYAIVYRRGWRAIAKALDIDEEDVPAIEVRAVKRNPLQPALYRILVRYGRVDLMPVTVDEVPPEMAGEFERLIERYDVPIDEKEERILEILRENPWTPHDEIARRLGLSVSEVEGEKDPESSGIYSLWSRVVVNIEYDERTAKRHVKRRDRLLEELYEHLEELSERYLRHPLTRRWIVEHKRDIMRRYLEQRIVECALKLQDRYGIREDVALCLARAFDGSISMIATTPYRTLKDVCPDLTLEEAKSVNRTLATLIDEHGLSPDAADELIEHFESIAGI 380
                                    13        23        33        43   | |  53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       
                                                                      47 |                                                                                                                                                                                                                                                                                                                                           
                                                                        49
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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 3M7D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M7D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3M7D)

(-) 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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(no "Cis Peptide Bonds" information available for 3m7d)
 

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 Related Entries

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

UniProtKB/TrEMBL
        Q977W1_9EURY | Q977W1: 2csb 2csd 3m6k 3m6z 3m7g 5hm5

(-) Related Entries Specified in the PDB File

3m6k STRUCTURE OF THE 44 KDA N-TERMINAL FRAGMENT OF TOPOISOMERASE V WITH GUANIDIUM HYDROCHLORIDE IN A DIFFERENT CRYSTALLIZATION CONDITION
3m6z STRUCTURE OF THE N-TERMINAL 44 KDA FRAGMENT OF TOPOISOMERASE V IN THE PRESENCE OF GUANIDIUM HYDROCHLORIDE
3m7g