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(-) Description

Title :  CRYSTAL STRUCTURE OF DEINOCOCCUS RADIODURANS TOPOISOMERASE IB
 
Authors :  A. Patel, S. Shuman, A. Mondragon
Date :  23 Nov 05  (Deposition) - 27 Dec 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Topoisomerase Ib, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Patel, S. Shuman, A. Mondragon
Crystal Structure Of A Bacterial Type Ib Dna Topoisomerase Reveals A Preassembled Active Site In The Absence Of Dna.
J. Biol. Chem. V. 281 6030 2006
PubMed-ID: 16368685  |  Reference-DOI: 10.1074/JBC.M512332200

(-) Compounds

Molecule 1 - TYPE I TOPOISOMERASE, PUTATIVE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET3C
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: TOPIB
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2F4Q)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F4Q)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:200 -Pro A:201
2Gly A:231 -Pro A:232

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2F4Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2F4Q)

(-) Exons   (0, 0)

(no "Exon" information available for 2F4Q)

(-) 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:309
 aligned with Q9RWH8_DEIRA | Q9RWH8 from UniProtKB/TrEMBL  Length:346

    Alignment length:336
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331      
         Q9RWH8_DEIRA     2 PSRTELLAEEYLRREGHDPQKFRYVHPDGTPYTDADGLARIARLAVPPAYQDVYVSPDAENELQAFGRDAAGRLQYRYHPDFVQAGALKKWQRLTRFAGALPTLKVATTADLRASGLPPRKVMALMTRLLHVARFRVGSDIYARQHKTYGLSTLRQRHVVVDGNTVTFRFKGKHGVSQHKATSDRTLAANMQKLLDLPGPWLFQTVDAGGGERRRIHSTELNAYLREVIGPFTAKDFRTWGGTLLAAEYLAQQGTESSERQAKKVLVDCVKFVADDLGNTPAVTRGSYICPVIFDRYLDGKVLDDYEPRTERQEAELEGLTRSEGALKRMLESERT 337
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh..eee.---..ee.--------------hhhhhhh......eeeee.......eeeeee.....eeeee.hhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...----------..hhhhhhhh.eeee..eeeeeee.hhh.eeeeeeehhhhhhhhhhhhh.......eee......eee.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhh..hhhhhh..hhhhhhh....hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2f4q A   2 PSRTELLAEEYLRRE---PQKFR--------------LARIARLAVPPAYQDVYVSPDAENELQAFGRDAAGRLQYRYHPDFVQAGALKKWQRLTRFAGALPTLKVATTADLRASGLPPRKVmALmTRLLHVARFRV----------TYGLSTLRQRHVVVDGNTVTFRFKGKHGVSQHKATSDRTLAANmQKLLDLPGPWLFQTVDAGGGERRRIHSTELNAYLREVIGPFTAKDFRTWGGTLLAAEYLAQQGTESSERQAKKVLVDCVKFVADDLGNTPAVTRGSYICPVIFDRYLDGKVLDDYEPRTERQEAELEGLTRSEGALKRmLESERT 337
                                    11    |   21  |      -       |41        51        61        71        81        91       101       111       121  |  | 131      |  -       151       161       171       181       191|      201       211       221       231       241       251       261       271       281       291       301       311       321       331      
                                         16  20  24             39                                                                                  124-MSE       138        149                                        192-MSE                                                                                                                                    331-MSE  
                                                                                                                                                       127-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 2F4Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2F4Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F4Q)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9RWH8_DEIRA | Q9RWH8)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003917    DNA topoisomerase type I activity    Catalysis of a DNA topological transformation by transiently cleaving one DNA strand at a time to allow passage of another strand; changes the linking number by +1 per catalytic cycle.
    GO:0003918    DNA topoisomerase type II (ATP-hydrolyzing) activity    Catalysis of a DNA topological transformation by transiently cleaving a pair of complementary DNA strands to form a gate through which a second double-stranded DNA segment is passed, after which the severed strands in the first DNA segment are rejoined; product release is coupled to ATP binding and hydrolysis; changes the linking number in multiples of 2.
    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:0006265    DNA topological change    The process in which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number.

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 Related Entries

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UniProtKB/TrEMBL
        Q9RWH8_DEIRA | Q9RWH8: 3m4a

(-) Related Entries Specified in the PDB File

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