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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TOPOISOMERASE VI HOLOENZYME FROM METHANOSARCINA MAZEI
 
Authors :  K. D. Corbett, P. Benedetti, J. M. Berger
Date :  28 May 07  (Deposition) - 10 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Topoisomerase, Dna-Binding, Spo11, Atpase, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. D. Corbett, P. Benedetti, J. M. Berger
Holoenzyme Assembly And Atp-Mediated Conformational Dynamic Of Topoisomerase Vi
Nat. Struct. Mol. Biol. V. 14 611 2007
PubMed-ID: 17603498  |  Reference-DOI: 10.1038/NSMB1264

(-) Compounds

Molecule 1 - TYPE II DNA TOPOISOMERASE VI SUBUNIT A
    Chains: A
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PST39 COEXPRESSION VECTOR
    Expression System Strain: BL21(DE3) RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TOP6A
    Organism Scientific: METHANOSARCINA MAZEI
    Organism Taxid: 2209
 
Molecule 2 - TYPE 2 DNA TOPOISOMERASE 6 SUBUNIT B
    Chains: B
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PST39 COEXPRESSION VECTOR
    Expression System Strain: BL21(DE3) RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TOP6B
    Organism Scientific: METHANOSARCINA MAZEI
    Organism Taxid: 2209
    Synonym: TYPE II DNA TOPOISOMERASE VI SUBUNIT B, TOPOVI-B

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2Q2E)

(-) Sites  (0, 0)

(no "Site" information available for 2Q2E)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q2E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Q2E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q2E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q2E)

(-) Exons   (0, 0)

(no "Exon" information available for 2Q2E)

(-) 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 A from PDB  Type:PROTEIN  Length:315
 aligned with TOP6A_METMA | Q8PUB7 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:353
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364   
          TOP6A_METMA    15 LAREKLLEIAEKIYNQFEEEVVPSVSLPSRTKANLEYSDESDVWVYGDRESERSAKTVKGAFQLLKTTYATDFLINEHLARNRGSTLRELYYISEGWDYAKFKEQGESDRLIEDLEILTSLQREYFHMRPEEDGATMFGPIEITEQTKRGERNIHCQKDVGEGGYQIPFNVENIEFQKHDASMIIAIETGGMYARLMENGFDEAYNAILVHLKGQPARSTRRIIKRMNEELGIPVAVFTDGDPWSYRIYASVAYGAIKSAHLSEFMATPAAKFLGLQPSDIVEYELSTDKLTEQDVSALRSELSDPRFESDYWKEQIQLQLDIGKKAEQQAFAGKGLDFVTEVYLPNRLKEMG 367
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------                        ---TP6A_N-2q2 eA01 A:71-143                                                 ---------------------    ---- -------------------------------------------------------------------------------------------------        ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh.......------------------------....hhhhhhhhh-hhhhhhhh.........eehhhhhhhh............hhhhhhhhhhhhh..hhhhh.ee.......ee............----....-........................eeee...hhhhhhhhh.........eee.....hhhhhhhhhhhh......eeee...hhhhhh.hhhhhh..--------...........................hhhhhhhhh.............hhhhhhhhhhh....hhhhhhhh......hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q2e A  15 LAREKLLEIAEKIYNQFEEEVVPSVSLPS------------------------SAKTVKGAFQLLK-TYATDFLINEHLARNRGSTLRELYYISEGWDYAKFKEQGESDRLIEDLEILTSLQREYFHMRPEEDGATMFGPIEITEQTKRG----HCQK-VGEGGYQIPFNVENIEFQKHDASMIIAIETGGMYARLMENGFDEAYNAILVHLKGQPARSTRRIIKRMNEELGIPVAVFTDGDPWSYRIYASVAYGA--------FMATPAAKFLGLQPSDIVEYELSTDKLTEQDVSALRSELSDPRFESDYWKEQIQLQLDIGKKAEQQAFAGKGLDFVTEVYLPNRLKEMG 367
                                    24        34        |-         -         -   |    74     | |84        94       104       114       124       134       144       154       164    |  174       184       194       204       214       224       234       244       254       264     |   -    |  284       294       304       314       324       334       344       354       364   
                                                       43                       68          80 |                                                                               164  169  | |                                                                                             270      279                                                                                        
                                                                                              82                                                                                       172 |                                                                                                                                                                                                 
                                                                                                                                                                                         174                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:582
 aligned with TOP6B_METMA | Q8PUB8 from UniProtKB/Swiss-Prot  Length:621

    Alignment length:606
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610      
          TOP6B_METMA    11 KKQKSISVAEFFEKNRQILGFDSAPRSLITTVKEAVDNALDACEEAGILPDILVQVERTGPDYVTVIIEDNGPGIVREQIPKVFAKLLYGSRFHALKQSRGQQGIGISAAVLYAQMTAGRHTKILSKTSPTAPAHYYELMINTSTNEPDILVDEVRDWFRPHGTQIELEMRAAYVKGRRQSIYEYLKATAIVNPHARITLIDPDGNEEVFERATDKMPEPAEEILPHPEGIELGTLMKMLHYTERQKLAPFLRYSFCKIGLLTAEEICKAAGLDPEIDPHALGRHEARKLIEAFEKVKIMAPPTDCLSPIGEDLIYRGLEKETTVDFIATSTRKPAVYSGNPFVVEVGMAYGGNLPKEEKISIMRFANRVPLLYQQGGCVTTHAVEDIKWKQYGLNQPGGGIPVGPVILLIHVASINVPFTSESKDAIADIPVIKEEIDLAIKEVARKLKHYLSKQSNLKKRREKEIIITKVLPKLAAKVAHVLEKDVPDINPVVAKIMGNLLVHRVIKNNGDGTVDVAIKVKNFGTSAYSFRVHEMLPCKVSGAKPEPKVVTMGNDYDYVWDISASAGSSKVLSYKIESASEEELQKLPQLIVEGIEEELVTGAK 616
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ----------------------HATPase_c-2q2eB01 B:33-182                                                                                                                            ------------------------------------------------------------------------     ---------  -----------------------------------------Topo-VIb_trans-2q2eB02 B:312-475                                                                                                                                    -----------------------------------------------------------    --------------   --------------------------------------------------       ---- Pfam domains
         Sec.struct. author .......hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh......eeee..eee...eeeeeee......hhhhhhhhhh.....--.....-.....hhhhhhhhhhhhhhh....eeee........eeee..............eee..........eeee............hhhhhhhhhhhh...eeee.......eeee....................hhhhhhhhhhhh.-----.........--hhhhhhhhhh....................hhhhhh..............hhhhhhhhhhhhh...eee......eee..eeeeeeeeeee...........eeeee...........hhhhhhhhhh....................eeeeee................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh..hhhhhh..............hhhhhhhhh..eeeeeee.......eeeeeee..----...eee..ee....---.....eee....eee.eee......eeee......hhhhh..........-------.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2q2e B  11 KKQKSISVAEFFEKNRQILGFDSAPRSLITTVKEAVDNALDACEEAGILPDILVQVERTGPDYVTVIIEDNGPGIVREQIPKVFAKLLYG--FHALK-SRGQQGIGISAAVLYAQMTAGRHTKILSKTSPTAPAHYYELMINTSTNEPDILVDEVRDWFRPHGTQIELEMRAAYVKGRRQSIYEYLKATAIVNPHARITLIDPDGNEEVFERATDKMPEPAEEILPHPEGIELGTLMKMLHYTE-----PFLRYSFCK--LLTAEEICKAAGLDPEIDPHALGRHEARKLIEAFEKVKIMAPPTDCLSPIGEDLIYRGLEKETTVDFIATSTRKPAVYSGNPFVVEVGMAYGGNLPKEEKISIMRFANRVPLLYQQGGCVTTHAVEDIKWKQYGLNQPGGGIPVGPVILLIHVASINVPFTSESKDAIADIPVIKEEIDLAIKEVARKLKHYLSKQSNLKKRREKEIIITKVLPKLAAKVAHVLEKDVPDINPVVAKIMGNLLVHRVIKNNGDGTVDVAIKVKN----AYSFRVHEMLPCKV---KPEPKVVTMGNDYDYVWDISASAGSSKVLSYKIESASEEELQKLPQLIVE-------TGAK 616
                                    20        30        40        50        60        70        80        90       100  |   |110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   |   260       | -|      280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530   |   540       550 |   | 560       570       580       590       600    |    -  |   
                                                                                                                   100  | 107 |                                                                                                                                              254   260     268  |                                                                                                                                                                                                                                                                    534  539          552 556                                              605     613   
                                                                                                                      103   109                                                                                                                                                               271
   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  (0, 0)

(no "SCOP Domain" information available for 2Q2E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Q2E)

(-) Pfam Domains  (3, 3)

Asymmetric Unit
(-)
Clan: His_Kinase_A (147)
(-)
Clan: S5 (103)
(-)
Clan: no clan defined [family: TP6A_N] (2)

(-) Gene Ontology  (15, 23)

Asymmetric Unit(hide GO term definitions)
Chain A   (TOP6A_METMA | Q8PUB7)
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:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0000737    DNA catabolic process, endonucleolytic    The chemical reactions and pathways resulting in the breakdown of DNA, involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides.
    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: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.
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.

Chain B   (TOP6B_METMA | Q8PUB8)
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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