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(-) Description

Title :  CRYSTAL STRUCTURE OF A BACTERIAL TOPOISOMERASE IB IN COMPLEX WITH DNA REVEALS A SECONDARY DNA BINDING SITE
 
Authors :  A. Patel, L. Yakovleva, S. Shuman, A. Mondragon
Date :  10 Mar 10  (Deposition) - 14 Jul 10  (Release) - 14 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,D,E
Keywords :  Type Ib, Topib, Protein-Dna Complex, Isomerase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Patel, L. Yakovleva, S. Shuman, A. Mondragon
Crystal Structure Of A Bacterial Topoisomerase Ib In Comple With Dna Reveals A Secondary Dna Binding Site.
Structure V. 18 725 2010
PubMed-ID: 20541510  |  Reference-DOI: 10.1016/J.STR.2010.03.007

(-) Compounds

Molecule 1 - PUTATIVE TYPE I TOPOISOMERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DR_0690
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299
 
Molecule 2 - DNA (5'-D(*GP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*C)-3')
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*GP*CP*GP*CP*CP*CP*TP*TP*AP*TP*TP*C)-3')
    Chains: E
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ADE

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:105 , LYS A:106 , THR A:109 , ARG A:129 , HIS A:132 , HOH A:356 , HOH A:535BINDING SITE FOR RESIDUE ACY A 804
2AC2SOFTWAREHIS A:132 , ASP A:163 , GLU A:325 , HOH A:362 , HOH A:539BINDING SITE FOR RESIDUE ACY A 805
3AC3SOFTWAREHOH D:14 , HOH D:15 , HOH D:266 , HOH E:122BINDING SITE FOR RESIDUE MG D 808

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M4A)

(-) 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 3M4A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3M4A)

(-) Exons   (0, 0)

(no "Exon" information available for 3M4A)

(-) 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:304
 aligned with Q9RWH8_DEIRA | Q9RWH8 from UniProtKB/TrEMBL  Length:346

    Alignment length:337
                                    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 PSRTELLAEEYLRREGHDPQKFRYVHPDGTPYTDADGLARIARLAVPPAYQDVYVSPDAENELQAFGRDAAGRLQYRYHPDFVQAGALKKWQRLTRFAGALPTLKVATTADLRASGLPPRKVMALMTRLLHVARFRVGSDIYARQHKTYGLSTLRQRHVVVDGNTVTFRFKGKHGVSQHKATSDRTLAANMQKLLDLPGPWLFQTVDAGGGERRRIHSTELNAYLREVIGPFTAKDFRTWGGTLLAAEYLAQQGTESSERQAKKVLVDCVKFVADDLGNTPAVTRGSYICPVIFDRYLDGKVLDDYEPRTERQEAELEGLTRSEGALKRMLESERTL 338
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------    --                        -----------------------------Topo isom_I-3m4a   A01 A:69-314                                                                                                                                                                                                                       ------------------------ Pfam domains
         Sec.struct. author .hhhhhhh----..------------------------hhhhhhh.....eeeee.......eeeeee...-.eeeee.hhhh---..hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhh.eeee..eeeeeee.hhh.eeeeee.hhhhhhhhhhhhh.......eee..-...eee.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhh..hhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m4a A   2 PSRTELLA----RR------------------------ARIARLAVPPAYQDVYVSPDAENELQAFGRDAA-RLQYRYHPDFV---ALKKWQRLTRFAGALPTLKVATTADLRASGLPPRKVMALMTRLLHVARFRVGSDIYARQHKTYGLSTLRQRHVVVDGNTVTFRFKGKHGVSQHKATSDRTLAANMQKLLDLPGPWLFQTVDA-GGERRRIHSTELNAYLREVIGPFTAKDFRTWGGTLLAAEYLAQQGTESSERQAKKVLVDCVKFVADDLGNTPAVTRGSYICPVIFDRYLDGKVLDDYEPRTERQEAELEGLTRSEGALKRMLESERTL 338
                                   | -  ||     -         -        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       
                                   9   14|                       40                              72 |        84  88                                                                                                                      209 |                                                                                                                               
                                        15                                                         74                                                                                                                                      211                                                                                                                               


Chain D from PDB  Type:DNA  Length:12
                                            
                 3m4a D   2 GAATAAGGGCGC  13
                                    11  


Chain E from PDB  Type:DNA  Length:12
                                            
                 3m4a E 110 GCGCCCTTATTC 121
                                   119
   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 3M4A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M4A)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: DNA-mend (28)

(-) 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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        Q9RWH8_DEIRA | Q9RWH8: 2f4q

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