1Z5C - JenaLib

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Asym./Biol. Unit (Jmol Viewer)

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

Title :   TOPOISOMERASE VI-B, ADP PI 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 :   2.20

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

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

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 16)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:42 , ADP A:1001 , PO4 A:3001 , HOH A:3028 , HOH A:3041	BINDING SITE FOR RESIDUE MG A 2001
2	AC2	SOFTWARE	GLU A:38 , GLY A:106 , MSE A:107 , TYR A:108 , GLY A:109 , LEU A:110 , GLY A:111 , LYS A:427 , ADP A:1001 , MG A:2001	BINDING SITE FOR RESIDUE PO4 A 3001
3	AC3	SOFTWARE	ASN B:42 , ADP B:1002 , PO4 B:3002 , HOH B:3030 , HOH B:3096	BINDING SITE FOR RESIDUE MG B 2002
4	AC4	SOFTWARE	GLU B:38 , GLY B:106 , MSE 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:3075	BINDING SITE FOR RESIDUE PO4 B 3002
5	AC5	SOFTWARE	ASN A:42 , ALA A:46 , ASP A:76 , ILE A:81 , ALA A:89 , PHE A:90 , SER A:96 , SER A:97 , LYS A:98 , GLY A:106 , MSE A:107 , TYR A:108 , GLY A:109 , VAL A:112 , LYS A:113 , MG A:2001 , PO4 A:3001 , HOH A:3002 , HOH A:3003 , HOH A:3006 , HOH A:3024 , HOH A:3028 , PHE B:7	BINDING SITE FOR RESIDUE ADP A 1001
6	AC6	SOFTWARE	PHE 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 , GLY B:106 , MSE B:107 , TYR B:108 , GLY B:109 , GLY B:111 , VAL B:112 , LYS B:113 , MG B:2002 , PO4 B:3002 , HOH B:3009 , HOH B:3014 , HOH B:3026 , HOH B:3096	BINDING SITE FOR RESIDUE ADP B 1002

(no "SS Bond" information available for 1Z5C)

(no "Cis Peptide Bond" information available for 1Z5C)

(no "SAP(SNP)/Variant" information available for 1Z5C)

(no "PROSITE Motif" information available for 1Z5C)

(no "Exon" information available for 1Z5C)

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 d1z5ca3 A:4-228 Topoisomerase VI-B subunit                                                                                                                                                                                       d1z5ca1 A:229-306 Topoisomerase VI-B subunit middle domain                    d1z5ca2 A:307-469 Topoisomerase VI-B subunit                                                                                                                        SCOP domains
               CATH domains 1z5cA01 A:4-220  [code=3.30.565.10, no name defined]                                                                                                                                                                     ---------1z5cA02 A:230-307  [code=1.10.8.50, no name defined]                          -------1z5cA03 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..............hhhhhhhhhhhhhh..eeeeee...eee..eeeeeeeeeee..........eeeeee..eee..hhhhhhhhhhhhhhhhhhhh.......eeeeeeeee...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z5c 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      
                                                                                                                                 107-MSE       121-MSE                                                                                                                                                                                                                                                                                         409-MSE                             445-MSE                    
                                                                                                                                                                                                                                                                                                                                                                                                                                                  412-MSE

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 d1z5cb3 B:4-228 Topoisomerase VI-B subunit                                                                                                                                                                                       d1z5cb1 B:229-306 Topoisomerase VI-B subunit middle domain                    d1z5cb2 B:307-463 Topoisomerase VI-B subunit                                                                                                                  SCOP domains
               CATH domains 1z5cB01 B:4-220  [code=3.30.565.10, no name defined]                                                                                                                                                                     ---------1z5cB02 B:230-307  [code=1.10.8.50, no name defined]                          -------1z5cB03 B:315-463  [code=3.30.230.10, no name defined]                                                                                                CATH domains
           Pfam domains (1) ------------------------HATPase_c-1z5cB03 B:28-177                                                                                                                            ------------------------------------------FbpA-1z5cB01 B:220-313                                                                        ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ------------------------HATPase_c-1z5cB04 B:28-177                                                                                                                            ------------------------------------------FbpA-1z5cB02 B:220-313                                                                        ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Topo-VIb_trans-1z5cB05 B:309-463                                                                                                                            Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Topo-VIb_trans-1z5cB06 B:309-463                                                                                                                            Pfam domains (4)
         Sec.struct. author ....ee.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee....eeeeeeee........hhhhhhhh..ee.............hhhhhhhhhhhhhh...eeeeee.....eeeeeeeeee....eeeeeeeeeee......eeeeeeeee.hhhhhhhhhhhhhhhhhhhh...eeeee.....eeee.....................hhhhhhhhhhh.....hhhhhhhhhh...hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh......hhhhh...hhhhhhhhhhhhhh..eeeeee...eee..eeeeeeeeeee..........eeeeee..eee..hhhhhhhhhhhhhhhhhhhh.......eeeeeeeee...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z5c 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
                                                                                                                                 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)

1a	FbpA-1z5cB01	B:220-313
1b	FbpA-1z5cB02	B:220-313

Clan: His_Kinase_A (147)

Family: HATPase_c (132)

Sulfolobus shibatae (7)

2a	HATPase_c-1z5cB03	B:28-177
2b	HATPase_c-1z5cB04	B:28-177

Clan: S5 (103)

Family: Topo-VIb_trans (8)

Sulfolobus shibatae (7)

3a	Topo-VIb_trans-1z5cB05	B:309-463
3b	Topo-VIb_trans-1z5cB06	B:309-463

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1z5c)

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	1z5c
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	TOP6B_SULSH \| O05207
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	5.99.1.3
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UniProtKB/Swiss-Prot
	TOP6B_SULSH \| O05207	:	1mu5 1mx0 1z59 1z5a 1z5b 2hkj 2zbk

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
1z5b	TOPOISOMERASE VI-B, ADP ALF4- BOUND DIMER FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 16)

Sites (6, 6)

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, 6)

CATH Domains (3, 6)

Pfam Domains (3, 6)

Gene Ontology (9, 9)

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