3L4K - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   TOPOISOMERASE II-DNA CLEAVAGE COMPLEX, METAL-BOUND

Authors :   B. H. Schmidt, A. B. Burgin, J. E. Deweese, N. Osheroff, J. M. Berger

Date :   20 Dec 09 (Deposition) - 26 May 10 (Release) - 16 Jun 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.98

Chains :   Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: A,D,E  (1x)

Keywords :   Topoisomerase, Protein-Dna Complex, Covalently Linked Complex, Dna Supercoiling, Dna Replication, Atp-Binding, Dna-Binding, Isomerase, Nucleotide-Binding, Nucleus, Phosphoprotein, Isomerase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. H. Schmidt, A. B. Burgin, J. E. Deweese, N. Osheroff, J. M. Berger
A Novel And Unified Two-Metal Mechanism For Dna Cleavage By Type Ii And Ia Topoisomerases.
Nature V. 465 641 2010
PubMed-ID: 20485342 | Reference-DOI: 10.1038/NATURE08974

Molecule 1 - DNA TOPOISOMERASE 2
	Chains	:	A
	EC Number	:	5.99.1.3
	Engineered	:	YES
	Expression System	:	SACCHAROMYCES CEREVISIAE
	Expression System Plasmid	:	PGAL
	Expression System Strain	:	BCY123
	Expression System Taxid	:	4932
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 421-1177
	Gene	:	N2244, TOP2, TOR3, YNL088W
	Organism Common	:	BREWER'S YEAST,LAGER BEER YEAST,YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	DNA TOPOISOMERASE II

*Molecule 2 - DNA (5'-D(PCPCPTPAPCPTPGPCPTPAPC)-3')**
	Chains	:	B
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 3 - DNA (5'-D(CPGPCPGPGPTPAPGPCPAPGPTPAPGPG)- 3')**
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 4 - DNA (5'-D(PGPGPAPTPGPAPCPGPAPTP)-3')**
	Chains	:	D
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 5 - DNA (5'-D(CPGPCPGPAPAPTPCPGPTPCPAPTPCPC)- 3')**
	Chains	:	E
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (1x)	:	A	B	C
Biological Unit 2 (1x)	:	A			D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	PTR	1	Mod. Amino Acid	O-PHOSPHOTYROSINE
2	TSP	1	Ligand/Ion	3'-THIO-THYMIDINE-5'-PHOSPHATE
3	ZN	8	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	PTR	1	Mod. Amino Acid	O-PHOSPHOTYROSINE
2	TSP	-1	Ligand/Ion	3'-THIO-THYMIDINE-5'-PHOSPHATE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	PTR	1	Mod. Amino Acid	O-PHOSPHOTYROSINE
2	TSP	1	Ligand/Ion	3'-THIO-THYMIDINE-5'-PHOSPHATE
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:735 , GLU A:808 , ASP A:809	BINDING SITE FOR RESIDUE ZN A 1
2	AC2	SOFTWARE	ZN A:4 , GLU A:449 , ASP A:526 , PTR A:782 , DC B:11 , TSP D:11	BINDING SITE FOR RESIDUE ZN A 3
3	AC3	SOFTWARE	ZN A:3 , ASP A:526 , ASP A:528 , LYS A:603	BINDING SITE FOR RESIDUE ZN A 4
4	AC4	SOFTWARE	HIS A:981 , GLU A:1175	BINDING SITE FOR RESIDUE ZN A 5
5	AC5	SOFTWARE	GLU A:615 , HIS A:623 , ASP A:859	BINDING SITE FOR RESIDUE ZN A 6
6	AC6	SOFTWARE	GLN A:553 , HIS A:628 , GLU A:669	BINDING SITE FOR RESIDUE ZN A 7
7	AC7	SOFTWARE	HIS A:736	BINDING SITE FOR RESIDUE ZN A 8
8	AC8	SOFTWARE	ZN A:3 , GLU A:449 , LYS A:477 , ASP A:530 , HIS A:736 , GLY A:737 , PTR A:782 , DC C:1 , DG C:5 , DT C:6 , DT D:10 , DC E:1 , DA E:5 , DA E:6	BINDING SITE FOR RESIDUE TSP D 11
9	AC9	SOFTWARE	DG C:4 , DG E:4	BINDING SITE FOR RESIDUE ZN E 16

(no "SS Bond" information available for 3L4K)

(no "Cis Peptide Bond" information available for 3L4K)

(no "SAP(SNP)/Variant" information available for 3L4K)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TOPRIM	PS50880	Toprim domain profile.	TOP2_YEAST	443-557	1	A:443-557
2	TOPOISOMERASE_II	PS00177	DNA topoisomerase II signature.	TOP2_YEAST	447-455	1	A:447-455

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TOPRIM	PS50880	Toprim domain profile.	TOP2_YEAST	443-557	1	A:443-557
2	TOPOISOMERASE_II	PS00177	DNA topoisomerase II signature.	TOP2_YEAST	447-455	1	A:447-455

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TOPRIM	PS50880	Toprim domain profile.	TOP2_YEAST	443-557	1	A:443-557
2	TOPOISOMERASE_II	PS00177	DNA topoisomerase II signature.	TOP2_YEAST	447-455	1	A:447-455

Asymmetric Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YNL088W	1	YNL088W.1	XIV:457706-461992	4287	TOP2_YEAST	1-1428	1428	1	A:421-1177 (gaps)	758

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:722
 aligned with TOP2_YEAST | P06786 from UniProtKB/Swiss-Prot  Length:1428

    Alignment length:758
                                                                                                                                                                                                                                                                                                                                                                                                    782                                                                                                                                                                                                                                                                                                                                                                                                           
                                                                                                                                                                                                                                                                                                                                                                                                  781 |                                                                                                                                                                                                                                                                                                                                                                                                           
                                   430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780| |    789       799       809       819       829       839       849       859       869       879       889       899       909       919       929       939       949       959       969       979       989       999      1009      1019      1029      1039      1049      1059      1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      1169        
          TOP2_YEAST    421 SRITNYPKLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLIINFLESSFPGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDYEKWREEESHKFTWKQKYYKGLGTSLAQEVREYFSNLDRHLKIFHSLQGNDKDYIDLAFSKKKADDRKEWLRQYEPGTVLDPTLKEIPISDFINKELILFSLADNIRSIPNVLDGFKPGQRKVLYGCFKKNLKSELKVAQLAPYVSECTAYHHGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAFGTRATGGKDAAAAR-YIYTELNKLTRKIFHPADDPLYKYIQEDEKTVEPEWYLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEELEQMHPWFRGWTGTIEEIEPLRYRMYGRIEQIGDNVLEITELPARTWTSTIKEYLLLGLSGNDKIKPWIKDMEEQHDDNIKFIITLSPEEMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYNSVNEILSEFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKELTVTNKPRNAIIQELENLGFPRFNKEGKPYYGSPNDEIAEQINDVKGATSDEEDEESSHEDTENVINGPEELYGTYEYLLGMRIWSLTKERYQKLLKQKQEKETELENLLKLSAKDIWNTDLKAFEVGYQEFLQRDAEAR 1177
               SCOP domains d3l4ka_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains --------3l4kA01 A:429-561,A:609-691  [code=3.40.50.670, no name defined]                                                                     3l4kA02 A:562-608                              3l4kA01 A:429-561,A:609-691  [code=3.40.50.670, no name defined]                   3l4kA03 A:692-860,A:974-988 Topoisomerase II, domain 5                                                                                                                    -----------3l4kA04 A:872-973  [code=3.30.1360.40, no name defined]                                               3l4kA03        3l4kA05 A:989-1177 Topoisomerase, domain 3                                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................eeeeeehhhhhhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhhhhhhhh........hhhhh...eeeee...hhhhhhhhhhhhhhhhhhh.........eeee....eeeee......eeee.hhhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhh.eeee.....hhhhhhhhhhh..hhhhhhhhhhhh...........ee.hhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.....eehhhhhhhhhhhh....hhhhhhhhhhhhhh..................................ee....hhhhhhhhhhhhhh.eee....eeee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhh................eeee....eeeee.eeeeee..eeeeee.....hhhhhhhhhhhhhhh.........eeee.......eeee.hhhhhhhhhhhhhhhhh..eeeee...eeee.....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...ee.....ee...------------------------------------......hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------TOPRIM  PDB: A:443-557 UniProt: 443-557                                                                            --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------TOPOISOME--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:421-1177 (gaps) UniProt: 1-1428 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Transcript 1
                3l4k A  421 SRITNYPKLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLIINFLESSFPGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDYEKWREEESHKFTWKQKYYKGLGTSLAQEVREYFSNLDRHLKIFHSLQGNDKDYIDLAFSKKKADDRKEWLRQYEPGTVLDPTLKEIPISDFINKELILFSLADNIRSIPNVLDGFKPGQRKVLYGCFKKNLKSELKVAQLAPYVSECTAYHHGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAFGTRATGGKDAAAARyYIYTELNKLTRKIFHPADDPLYKYIQEDEKTVEPEWYLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEELEQMHPWFRGWTGTIEEIEPLRYRMYGRIEQIGDNVLEITELPARTWTSTIKEYLLLGLSGNDKIKPWIKDMEEQHDDNIKFIITLSPEEMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYNSVNEILSEFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKELTVTNKPRNAIIQELENLGFPRFNKEGKPYYGS------------------------------------EELYGTYEYLLGMRIWSLTKERYQKLLKQKQEKETELENLLKLSAKDIWNTDLKAFEVGYQEFLQRDAEAR 1177
                                   430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780 |     789       799       809       819       829       839       849       859       869       879       889       899       909       919       929       939       949       959       969       979       989       999      1009      1019      1029      1039      1049      1059      1069|        -         -         -      1109      1119      1129      1139      1149      1159      1169        
                                                                                                                                                                                                                                                                                                                                                                                                   782-PTR                                                                                                                                                                                                                                                                                         1070                                 1107

Chain B from PDB  Type:DNA  Length:11
                                            
                3l4k B    1 CCTACTGCTAC   11
                                    10

Chain C from PDB  Type:DNA  Length:15
                                                
                3l4k C    1 CGCGGTAGCAGTAGG   15
                                    10

Chain D from PDB  Type:DNA  Length:10
                                           
                3l4k D    1 GGATGACGAT   10
                                    10

Chain E from PDB  Type:DNA  Length:15
                                                
                3l4k E    1 CGCGAATCGTCATCC   15
                                    10

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 '\|'

(no "Pfam Domain" information available for 3L4K)

Asymmetric Unit(hide GO term definitions)

Chain A (TOP2_YEAST | P06786)

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: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.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0006271	DNA strand elongation involved in DNA replication	The process in which a DNA strand is synthesized from template DNA during replication by the action of polymerases, which add nucleotides to the 3' end of the nascent DNA strand.
	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.
	GO:0006333	chromatin assembly or disassembly	The formation or destruction of chromatin structures.
	GO:0031055	chromatin remodeling at centromere	Dynamic structural changes in centromeric DNA.
	GO:0044774	mitotic DNA integrity checkpoint	A mitotic cell cycle process that controls cell cycle progression in response to changes in DNA structure by monitoring the integrity of the DNA. The DNA integrity checkpoint begins with detection of DNA damage, defects in DNA structure or DNA replication, and ends with signal transduction.
	GO:0007131	reciprocal meiotic recombination	The cell cycle process in which double strand breaks are formed and repaired through a double Holliday junction intermediate. This results in the equal exchange of genetic material between non-sister chromatids in a pair of homologous chromosomes. These reciprocal recombinant products ensure the proper segregation of homologous chromosomes during meiosis I and create genetic diversity.
	GO:0000019	regulation of mitotic recombination	Any process that modulates the frequency, rate or extent of DNA recombination during mitosis.
	GO:0097046	replication fork progression beyond termination site	Regulation of DNA replication by a mechanism that allows a DNA replication fork to progress beyond a termination site, which is a region containing fork pausing elements that influence the progression and merging of DNA replication forks.
	GO:0000712	resolution of meiotic recombination intermediates	The cleavage and rejoining of intermediates, such as Holliday junctions, formed during meiotic recombination to produce two intact molecules in which genetic material has been exchanged.
	GO:0000819	sister chromatid segregation	The cell cycle process in which sister chromatids are organized and then physically separated and apportioned to two or more sets.
cellular component
	GO:0097047	DNA replication termination region	A chromosomal region that contains fork pausing elements influencing the progression and merging of DNA replication forks.
	GO:0009330	DNA topoisomerase complex (ATP-hydrolyzing)	Complex that possesses DNA topoisomerase (ATP-hydrolyzing) activity.
	GO:0009295	nucleoid	The region of a virus, bacterial cell, mitochondrion or chloroplast to which the nucleic acid is confined.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0000795	synaptonemal complex	A proteinaceous scaffold found between homologous chromosomes during meiosis. It consists of 2 lateral elements and a central element, all running parallel to each other. Transverse filaments connect the lateral elements to the central element.

Asymmetric Unit
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	Cis Peptide Bonds
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Access by PDB/NDB ID
	3l4k
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	5.99.1.3
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	TOP2_YEAST \| P06786	:	1bgw 1bjt 1pvg 1qzr 2rgr 3l4j 4gfh

3l4j	THE SAME PROTEIN WITHOUT ZINC IONS SOAKED IN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (1, 1)

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Related Entries Specified in the PDB File