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(-) Description

Title :  CRYSTAL STRUCTURE OF CATALYTIC CORE OF A. BAUMANNII TOPO IV (PARE-PARC FUSION TRUNCATE)
 
Authors :  A. Wohlkonig, P. F. Chan, A. P. Fosberry, P. Homes, J. Huang, M. Kranz, V. T. J. Miles, N. D. Pearson, R. L. Perera, A. J. Shillings, M. N. Gwynn, B.
Date :  08 Jul 10  (Deposition) - 01 Sep 10  (Release) - 25 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  E
Biol. Unit 1:  E  (2x)
Keywords :  Isomerase, Type Iia Topoisomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Wohlkonig, P. F. Chan, A. P. Fosberry, P. Homes, J. Huang, M. Kranz, V. R. Leydon, T. J. Miles, N. D. Pearson, R. L. Perera, A. J. Shillings, M. N. Gwynn, B. D. Bax
Structural Basis Of Quinolone Inhibition Of Type Iia Topoisomerases And Target-Mediated Resistance
Nat. Struct. Mol. Biol. V. 17 1152 2010
PubMed-ID: 20802486  |  Reference-DOI: 10.1038/NSMB.1892

(-) Compounds

Molecule 1 - TOPOISOMERASE IV
    Chains: E
    EC Number: 5.99.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET22B
    Expression System Vector Type: PLASMID
    Fragment: PARE SUBUNIT C-TERMINAL 28KDA DOMAIN, RESIDUES 370-627, PARC SUBUNIT N-TERMINAL 58KDA DOMAIN, RESIDUES 1 TO 503
    Organism Scientific: ACINETOBACTER BAUMANNII
    Organism Taxid: 470
    Other Details: THE CONSTRUCT IS A FUSION OF THE TOPO IV, PARE AND PARC SUBUNITS. RESIDUE 604 OF PARE IS LINKED TO RESIDUES 996 OF PARC
    Strain: EUROFINS MEDINET

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : E
Biological Unit 1 (2x): E

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG E:1201 , LYS E:1470BINDING SITE FOR RESIDUE SO4 E2494
2AC2SOFTWARELYS E:584 , ARG E:585BINDING SITE FOR RESIDUE SO4 E2602
3AC3SOFTWARETRP E:1147 , LYS E:1156BINDING SITE FOR RESIDUE GOL E2495

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2XKJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XKJ)

(-) Sequences/Alignments

Asymmetric 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 E from PDB  Type:PROTEIN  Length:721
 aligned with B0VP98_ACIBS | B0VP98 from UniProtKB/TrEMBL  Length:739

    Alignment length:721
                                                                                                                                                                                                                                           1 3      4  7               8                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
                                     -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -       | 3      |  7         -     |  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       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492 
        B0VP98_ACIBS      - ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MTS------LAHH---------------ATENRSVAEFTEQAYLNYAMYVIMDRALPHISDGLKPVQRRIVYAMSELGLKSSGKPKKSARTVGDVLGKYHPHGDSACYEAMVLMAQPFSYRYPLIEGQGNWGSPDDPKSFAAMRYTEAKLSAYSELLLSELGQGTSEWQDNFDGSLKEPITLPARVPNILLNGTTGIAVGMATDIPPHNLREVVKGTIALIRNPQTSDEKLAEYIPAPDLPTKAEIITPPEELLKIQTTGRGSYRMRAVYTIEKNEIVITELPYQVSGSKVITQIADQMQAKKLPLVVDVRDESDHENPTRLVIVLRSNRIDAEAVMSHLFATTDLESSYRVNLNMIGEDGRPQVKSIRRILLEWIEIRKKTVTRRLQYHLNRIEKRLHILAGLLIAYLDIDTVIRIIREEDQPKPVLMEHFNIDEIQAEAILELKLRHLAKLEEMEIRHEQDELSAKAAIIREQLENPESLKNLIISELKEDAKKFGDERRSPIVARAEAVQI  493
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_topoisoIV-2xkjE01 E:1033-1470                                                                                                                                                                                                                                                                                                                                                                                                                     ----------------------- Pfam domains
         Sec.struct. author ....................hhhh.eeeeeehhhhhhhhhhhh....eeeeee.............hhhh.hhhhhhhhhhh..............eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....eeeee..eeeee.hhhhhhhhhhh.......eeee..hhhh.hhhhhhhhhh......eeeee..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..eeehhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh........eehhhhhhhhhhhh...hhhhhhhhhhhhhh........ee....................eeee...hhhhhh........eee......eee.......hhhhhhheeeee..eeeee...hhhhhhhhhhhhhhh...hhhhhhhhh.........ee..hhhhhhhhhhhheeeeeee.eeeee..eeeeee.....hhhhhhhhhhhhhhh.....eeeeee.........eeeee.....hhhhhhhhhhhhh..eeeeeee.eee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2xkj E  364 ERKKIVSGPALPGKLADCVGTREESELFIVEGDSAGGSAKQARDKNFQAIMPIRGKILNTWEVSSDEVLASQEVHDIAIAIGVDPGSDDLSELRYGKICILADADSDGLHIATLLCALFVKHFPALVEEGHLYVAMPPLFRIDIGKDVHYALDDEELETILKNVKGNKNPQITRFKGLGEMNAIQLRETTMDPNTRRLVQLDLDDAHLTAGLLDKLLAKKRAADRKQWLEQKGNLADENRSVAEFTEQAYLNYAMYVIMDRALPHISDGLKPVQRRIVYAMSELGLKSSGKPKKSARTVGDVLGKYHPHGDSACYEAMVLMAQPFSYRYPLIEGQGNWGSPDDPKSFAAMRYTEAKLSAYSELLLSELGQGTSEWQDNFDGSLKEPITLPARVPNILLNGTTGIAVGMATDIPPHNLREVVKGTIALIRNPQTSDEKLAEYIPAPDLPTKAEIITPPEELLKIQTTGRGSYRMRAVYTIEKNEIVITELPYQVSGSKVITQIADQMQAKKLPLVVDVRDESDHENPTRLVIVLRSNRIDAEAVMSHLFATTDLESSYRVNLNMIGEDGRPQVKSIRRILLEWIEIRKKTVTRRLQYHLNRIEKRLHILAGLLIAYLDIDTVIRIIREEDQPKPVLMEHFNIDEIQAEAILELKLRHLAKLEEMEIRHEQDELSAKAAIIREQLENPESLKNLIISELKEDAKKFGDERRSPIVARAEAVQI 1493
                                   373       383|      394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594      1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152      1162      1172      1182      1192      1202      1212      1222      1232      1242      1252      1262      1272      1282      1292      1302      1312      1322      1332      1342      1352      1362      1372      1382      1392      1402      1412      1422      1432      1442      1452      1462      1472      1482      1492 
                                             383|                                                                                                                                                                                                                     601|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
                                              385                                                                                                                                                                                                                     1010
   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 2XKJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: DNA_topoisoIV] (19)

(-) Gene Ontology  (15, 23)

Asymmetric Unit(hide GO term definitions)
Chain E   (B0VP98_ACIBS | B0VP98)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003916    DNA topoisomerase activity    Catalysis of the transient cleavage and passage of individual DNA strands or double helices through one another, resulting a topological transformation in double-stranded DNA.
    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:0006259    DNA metabolic process    Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
    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.
    GO:0007059    chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0019897    extrinsic component of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

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        B0V9T6_ACIBY | B0V9T6: 2xkk
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(-) Related Entries Specified in the PDB File

2xkk CRYSTAL STRUCTURE OF MOXIFLOXACIN, DNA, AND A. BAUMANNII TOPO IV (PARE-PARC FUSION TRUNCATE)