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(-) Description

Title :  TOPOISOMERASE VI-B, ADP ALF4- BOUND DIMER FORM
 
Authors :  K. D. Corbett, J. M. Berger
Date :  17 Mar 05  (Deposition) - 14 Jun 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Topoisomerase, Archaea, Atpase, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. D. Corbett, J. M. Berger
Structural Dissection Of Atp Turnover In The Prototypical Ghl Atpase Topovi.
Structure V. 13 873 2005
PubMed-ID: 15939019  |  Reference-DOI: 10.1016/J.STR.2005.03.013

(-) Compounds

Molecule 1 - TYPE II DNA TOPOISOMERASE VI SUBUNIT B
    Chains: A, B
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Gene: TOP6B
    Organism Scientific: SULFOLOBUS SHIBATAE
    Organism Taxid: 2286
    Synonym: TOPOVI-B

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ALF2Ligand/IonTETRAFLUOROALUMINATE ION
3MG3Ligand/IonMAGNESIUM ION
4SO41Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:42 , ADP A:1001 , ALF A:3001 , HOH A:4038 , HOH A:4136BINDING SITE FOR RESIDUE MG A 2001
2AC2SOFTWAREGLU A:38 , GLY A:106 , MET A:107 , TYR A:108 , GLY A:109 , LEU A:110 , GLY A:111 , LYS A:427 , ADP A:1001 , MG A:2001 , HOH A:4002 , HOH A:4038 , HOH A:4136 , HOH A:4137BINDING SITE FOR RESIDUE ALF A 3001
3AC3SOFTWAREASN B:42 , ADP B:1002 , ALF B:3002 , HOH B:3008 , HOH B:3165BINDING SITE FOR RESIDUE MG B 2002
4AC4SOFTWAREGLU B:38 , GLY B:106 , MET B:107 , TYR B:108 , GLY B:109 , LEU B:110 , GLY B:111 , LYS B:427 , ADP B:1002 , MG B:2002 , HOH B:3003 , HOH B:3008 , HOH B:3089 , HOH B:3165BINDING SITE FOR RESIDUE ALF B 3002
5AC5SOFTWAREGLY A:266 , ASP A:267 , THR A:268 , THR A:269 , ARG A:307 , HOH A:4005 , ARG B:307BINDING SITE FOR RESIDUE SO4 A 4001
6AC6SOFTWAREARG B:102 , THR B:418 , HOH B:3030 , HOH B:3069BINDING SITE FOR RESIDUE MG B 2003
7AC7SOFTWAREASN A:42 , ALA A:46 , ASP A:76 , GLY A:80 , ILE A:81 , ALA A:89 , TYR A:95 , SER A:96 , SER A:97 , LYS A:98 , GLY A:106 , MET A:107 , TYR A:108 , GLY A:109 , LEU A:110 , GLY A:111 , VAL A:112 , LYS A:113 , MG A:2001 , ALF A:3001 , HOH A:4004 , HOH A:4009 , HOH A:4011 , HOH A:4012 , HOH A:4136 , PHE B:7BINDING SITE FOR RESIDUE ADP A 1001
8AC8SOFTWAREPHE A:7 , ASN B:42 , ALA B:46 , ASP B:76 , GLY B:80 , ILE B:81 , ALA B:89 , TYR B:95 , SER B:96 , SER B:97 , LYS B:98 , MET B:107 , TYR B:108 , GLY B:109 , LEU B:110 , GLY B:111 , VAL B:112 , LYS B:113 , THR B:170 , MG B:2002 , ALF B:3002 , HOH B:3007 , HOH B:3008 , HOH B:3010 , HOH B:3016 , HOH B:3165BINDING SITE FOR RESIDUE ADP B 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z5B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Z5B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z5B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Z5B)

(-) Exons   (0, 0)

(no "Exon" information available for 1Z5B)

(-) 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:466
 aligned with TOP6B_SULSH | O05207 from UniProtKB/Swiss-Prot  Length:530

    Alignment length:466
                                    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       383       393       403       413       423       433       443       453       463      
          TOP6B_SULSH     4 KEKFTSLSPAEFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQTRGMYGLGVKAAVLYSQMHQDKPIEIETSPVNSKRIYTFKLKIDINKNEPIIVERGSVENTRGFHGTSVAISIPGDWPKAKSRIYEYIKRTYIITPYAEFIFKDPEGNVTYYPRLTNKIPKPPQEVKPHPYGVDREEIKILINNLKRDYTIKEFLVNEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKKDEDFRSPSADSLSVIGEDLIELGLKKIFNPDFAASITRKPKAYQGHPFIVEAGVAFGGSIPVGEEPIVLRYANKIPLIYDEKSDVIWKVVEELDWKRYGIESDQYQMVVMVHLCSTKIPYKSAGKESIAEVENIEKEIKNALMEVARKLKQYLSEKRKEQEAKKKLL 469
               SCOP domains d1z5ba3 A:4-228 Topoisomerase VI-B subunit                                                                                                                                                                                       d1z5ba1 A:229-306 Topoisomerase VI-B subunit middle domain                    d1z5ba2 A:307-469 Topoisomerase VI-B subunit                                                                                                                        SCOP domains
               CATH domains 1z5bA01 A:4-220  [code=3.30.565.10, no name defined]                                                                                                                                                                     ---------1z5bA02 A:230-307  [code=1.10.8.50, no name defined]                          -------1z5bA03 A:315-469  [code=3.30.230.10, no name defined]                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee....eeeeeeee.....hhhhhhhhhhh..ee.............hhhhhhhhhhhhhh...eeeeee.....eeeeeeeeee....eeeeeeeeeee......eeeeeeeee.hhhhhhhhhhhhhhhhhhhh...eeeee.....eeee.....................hhhhhhhhhhh.....hhhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh......hhhhh...hhhhhhhhhhhhhh..eeeeee...eee..eeeeeeeeeee..........eeeeee..eee..hhhhhhhhhhhhhhhhhhhh.......eeeeeeeee...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z5b A   4 KEKFTSLSPAEFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQTRGMYGLGVKAAVLYSQMHQDKPIEIETSPVNSKRIYTFKLKIDINKNEPIIVERGSVENTRGFHGTSVAISIPGDWPKAKSRIYEYIKRTYIITPYAEFIFKDPEGNVTYYPRLTNKIPKPPQEVKPHPYGVDREEIKILINNLKRDYTIKEFLVNEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKKYEDFRSPSADSLSVIGEDLIELGLKKIFNPDFAASITRKPKAYQGHPFIVEAGVAFGGSIPVGEEPIVLRYANKIPLIYDEKSDVIWKVVEELDWKRYGIESDQYQMVVMVHLCSTKIPYKSAGKESIAEVEDIEKEIKNALMEVARKLKQYLSEKRKEQEAKKKLL 469
                                    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       383       393       403       413       423       433       443       453       463      


Chain B from PDB  Type:PROTEIN  Length:460
 aligned with TOP6B_SULSH | O05207 from UniProtKB/Swiss-Prot  Length:530

    Alignment length:460
                                    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       383       393       403       413       423       433       443       453       463
          TOP6B_SULSH     4 KEKFTSLSPAEFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQTRGMYGLGVKAAVLYSQMHQDKPIEIETSPVNSKRIYTFKLKIDINKNEPIIVERGSVENTRGFHGTSVAISIPGDWPKAKSRIYEYIKRTYIITPYAEFIFKDPEGNVTYYPRLTNKIPKPPQEVKPHPYGVDREEIKILINNLKRDYTIKEFLVNEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKKDEDFRSPSADSLSVIGEDLIELGLKKIFNPDFAASITRKPKAYQGHPFIVEAGVAFGGSIPVGEEPIVLRYANKIPLIYDEKSDVIWKVVEELDWKRYGIESDQYQMVVMVHLCSTKIPYKSAGKESIAEVENIEKEIKNALMEVARKLKQYLSEKRKEQE 463
               SCOP domains d1z5bb3 B:4-228 Topoisomerase VI-B subunit                                                                                                                                                                                       d1z5bb1 B:229-306 Topoisomerase VI-B subunit middle domain                    d1z5bb2 B:307-463 Topoisomerase VI-B subunit                                                                                                                  SCOP domains
               CATH domains 1z5bB01 B:4-220  [code=3.30.565.10, no name defined]                                                                                                                                                                     ---------1z5bB02 B:230-307  [code=1.10.8.50, no name defined]                          -------1z5bB03 B:315-463  [code=3.30.230.10, no name defined]                                                                                                CATH domains
           Pfam domains (1) ------------------------HATPase_c-1z5bB03 B:28-177                                                                                                                            ------------------------------------------FbpA-1z5bB01 B:220-313                                                                        ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ------------------------HATPase_c-1z5bB04 B:28-177                                                                                                                            ------------------------------------------FbpA-1z5bB02 B:220-313                                                                        ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Topo-VIb_trans-1z5bB05 B:309-463                                                                                                                            Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Topo-VIb_trans-1z5bB06 B:309-463                                                                                                                            Pfam domains (4)
         Sec.struct. author ....ee.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee....eeeeeeee.....hhhhhhhhhhh..ee.............hhhhhhhhhhhhhh...eeeeee.....eeeeeeeeee....eeeeeeeeeee......eeeeeeeee.hhhhhhhhhhhhhhhhhhhh...eeeee.....eeee.....................hhhhhhhhhhh.....hhhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh......hhhhh...hhhhhhhhhhhhhh..eeeeee...eee..eeeeeeeeeee..........eeeeee..eee..hhhhhhhhhhhhhhhhhhhh.......eeeeeeeee...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z5b B   4 KEKFTSLSPAEFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQTRGMYGLGVKAAVLYSQMHQDKPIEIETSPVNSKRIYTFKLKIDINKNEPIIVERGSVENTRGFHGTSVAISIPGDWPKAKSRIYEYIKRTYIITPYAEFIFKDPEGNVTYYPRLTNKIPKPPQEVKPHPYGVDREEIKILINNLKRDYTIKEFLVNEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKKYEDFRSPSADSLSVIGEDLIELGLKKIFNPDFAASITRKPKAYQGHPFIVEAGVAFGGSIPVGEEPIVLRYANKIPLIYDEKSDVIWKVVEELDWKRYGIESDQYQMVVMVHLCSTKIPYKSAGKESIAEVEDIEKEIKNALMEVARKLKQYLSEKRKEQE 463
                                    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       383       393       403       413       423       433       443       453       463
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (3, 6)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Clan: H2TH (43)
(-)
Family: FbpA (7)
(-)
Sulfolobus shibatae (7)
1aFbpA-1z5bB01B:220-313
1bFbpA-1z5bB02B:220-313
(-)
Clan: His_Kinase_A (147)
(-)
Clan: S5 (103)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TOP6B_SULSH | O05207)
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.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
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.
    GO:0006268    DNA unwinding involved in DNA replication    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating unpaired template strands for DNA replication.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TOP6B_SULSH | O05207: 1mu5 1mx0 1z59 1z5a 1z5c 2hkj 2zbk

(-) Related Entries Specified in the PDB File

1mu5 TOPOISOMERASE VI-B, APO MONOMER FORM
1mx0 TOPOISOMERASE VI-B, AMPPNP-BOUND DIMER FORM
1z59 TOPOISOMERASE VI-B, ADP-BOUND MONOMER FORM
1z5a TOPOISOMERASE VI-B, ADP-BOUND DIMER FORM
1z5c TOPOISOMERASE VI-B, ADP PI BOUND DIMER FORM