1Z59 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   TOPOISOMERASE VI-B, ADP-BOUND MONOMER 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 :   2.10

Chains :   Asym./Biol. Unit : A

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

Molecule 1 - TYPE II DNA TOPOISOMERASE VI SUBUNIT B
	Chains	:	A
	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

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 7)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	MSE	5	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:42 , ADP A:2001 , HOH A:2015 , HOH A:2059 , HOH A:2084	BINDING SITE FOR RESIDUE MG A 1001
2	AC2	SOFTWARE	ASN A:42 , ALA A:46 , ASP A:76 , GLY A:80 , ILE A:81 , ALA A:89 , LEU A:110 , VAL A:112 , LYS A:113 , THR A:170 , MG A:1001 , HOH A:2006 , HOH A:2013 , HOH A:2015 , HOH A:2059 , HOH A:2069 , HOH A:2112	BINDING SITE FOR RESIDUE ADP A 2001

(no "SS Bond" information available for 1Z59)

(no "Cis Peptide Bond" information available for 1Z59)

(no "SAP(SNP)/Variant" information available for 1Z59)

(no "PROSITE Motif" information available for 1Z59)

(no "Exon" information available for 1Z59)

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:462
 aligned with TOP6B_SULSH | O05207 from UniProtKB/Swiss-Prot  Length:530

    Alignment length:462
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468  
          TOP6B_SULSH     9 SLSPAEFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQTRGMYGLGVKAAVLYSQMHQDKPIEIETSPVNSKRIYTFKLKIDINKNEPIIVERGSVENTRGFHGTSVAISIPGDWPKAKSRIYEYIKRTYIITPYAEFIFKDPEGNVTYYPRLTNKIPKPPQEVKPHPYGVDREEIKILINNLKRDYTIKEFLVNEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKKDEDFRSPSADSLSVIGEDLIELGLKKIFNPDFAASITRKPKAYQGHPFIVEAGVAFGGSIPVGEEPIVLRYANKIPLIYDEKSDVIWKVVEELDWKRYGIESDQYQMVVMVHLCSTKIPYKSAGKESIAEVENIEKEIKNALMEVARKLKQYLSEKRKEQEAKKKLLA 470
               SCOP domains d1z59a3 A:9-228 Topoisomerase VI-B subunit                                                                                                                                                                                  d1z59a1 A:229-306 Topoisomerase VI-B subunit middle domain                    d1z59a2 A:307-470 Topoisomerase VI-B subunit                                                                                                                         SCOP domains
               CATH domains 1z59A01 A:9-220  [code=3.30.565.10, no name defined]                                                                                                                                                                ---------1z59A02 A:230-307  [code=1.10.8.50, no name defined]                          -------1z59A03 A:315-470  [code=3.30.230.10, no name defined]                                                                                                       CATH domains
           Pfam domains (1) -------------------HATPase_c-1z59A02 A:28-177                                                                                                                            ------------------------------------------FbpA-1z59A01 A:220-313                                                                        ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Topo-VIb_trans-1z59A03 A:309-467                                                                                                                               --- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee....eeeeeee......hhhhhhhhhhh..................hhhhhhhhhhhhh...eeeeee.....eeeeeeeee......eeeeeeeeee......eeeeeeeee.hhhhhhhhhhhhhhhhhhhh...eeeee.....eeee................hhhhhhhhhhhhhhhhh....hhhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh......hhhhh...hhhhhhhhhhhhhh..eeeeee...eee..eeeeeeeeeee..........eeeeee..eee..hhhhhhhhhhhhhhhhhhhh.......eeeeeeeee...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1z59 A   9 SLSPAEFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQTRGmYGLGVKAAVLYSQmHQDKPIEIETSPVNSKRIYTFKLKIDINKNEPIIVERGSVENTRGFHGTSVAISIPGDWPKAKSRIYEYIKRTYIITPYAEFIFKDPEGNVTYYPRLTNKIPKPPQEVKPHPYGVDREEIKILINNLKRDYTIKEFLVNEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKKYEDFRSPSADSLSVIGEDLIELGLKKIFNPDFAASITRKPKAYQGHPFIVEAGVAFGGSIPVGEEPIVLRYANKIPLIYDEKSDVIWKVVEELDWKRYGIESDQYQmVVmVHLCSTKIPYKSAGKESIAEVEDIEKEIKNALmEVARKLKQYLSEKRKEQEAKKKLLA 470
                                    18        28        38        48        58        68        78        88        98       108       118  |    128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408|  |   418       428       438      |448       458       468  
                                                                                                                            107-MSE       121-MSE                                                                                                                                                                                                                                                                                         409-MSE                             445-MSE                     
                                                                                                                                                                                                                                                                                                                                                                                                                                             412-MSE

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 '\|'

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: H2TH (43)

Family: FbpA (7)

Sulfolobus shibatae (7)

FbpA-1z59A01

A:220-313

Clan: His_Kinase_A (147)

Family: HATPase_c (132)

Sulfolobus shibatae (7)

HATPase_c-1z59A02

A:28-177

Clan: S5 (103)

Family: Topo-VIb_trans (8)

Sulfolobus shibatae (7)

Topo-VIb_trans-1z59A03

A:309-467

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1z59)

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Access by PDB/NDB ID
	1z59
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	5.99.1.3
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	TOP6B_SULSH \| O05207
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UniProtKB/Swiss-Prot
	TOP6B_SULSH \| O05207	:	1mu5 1mx0 1z5a 1z5b 1z5c 2hkj 2zbk

1mu5	TOPOISOMERASE VI-B, APO MONOMER FORM
1mx0	TOPOISOMERASE VI-B, AMPPNP-BOUND DIMER FORM
1z5a	TOPOISOMERASE VI-B, ADP-BOUND DIMER FORM
1z5b	TOPOISOMERASE VI-B, ADP ALF4- BOUND DIMER FORM
1z5c	TOPOISOMERASE VI-B, ADP PI BOUND DIMER FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 3)

CATH Domains (3, 3)

Pfam Domains (3, 3)

Gene Ontology (9, 9)

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