2RGR - JenaLib

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Title :   TOPOISOMERASE IIA BOUND TO G-SEGMENT DNA

Authors :   K. C. Dong, J. M. Berger

Date :   04 Oct 07 (Deposition) - 25 Dec 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

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

Reference :   K. C. Dong, J. M. Berger
Structural Basis For Gate-Dna Recognition And Bending By Type Iia Topoisomerases.
Nature V. 450 1201 2007
PubMed-ID: 18097402 | Reference-DOI: 10.1038/NATURE06396
(for further references see the PDB file header)

Molecule 1 - DNA TOPOISOMERASE 2
	Chains	:	A
	EC Number	:	5.99.1.3
	Engineered	:	YES
	Expression System	:	SACCHAROMYCES CEREVISIAE
	Expression System Common	:	BAKER'S YEAST
	Expression System Plasmid	:	PGAL
	Expression System Strain	:	BCY123
	Expression System Taxid	:	4932
	Expression System Vector Type	:	PLASMID
	Fragment	:	DNA BINDING AND CLEAVAGE DOMAIN (RESIDUES 419- 1177)
	Gene	:	TOP2, TOR3
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	DNA TOPOISOMERASE II

Molecule 2 - DNA
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - DNA
	Chains	:	D
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3
Asymmetric Unit	:	A	C	D
Biological Unit 1 (2x)	:	A	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:30 , HOH A:31 , HOH A:32 , GLU A:449 , ASP A:526 , ASP A:528 , HOH C:45	BINDING SITE FOR RESIDUE MG A 1

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

Asymmetric Unit

No.	Residues
1	Arg A:482	-	Glu A:483
2	Lys A:570	-	Pro A:571

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

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, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TOPRIM	PS50880	Toprim domain profile.	TOP2_YEAST	443-557	2	A:443-557
2	TOPOISOMERASE_II	PS00177	DNA topoisomerase II signature.	TOP2_YEAST	447-455	2	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:419-1177 (gaps)	759

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
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Chain A from PDB  Type:PROTEIN  Length:721
 aligned with TOP2_YEAST | P06786 from UniProtKB/Swiss-Prot  Length:1428

    Alignment length:759
                                   428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008      1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138      1148      1158      1168         
          TOP2_YEAST    419 RKSRITNYPKLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLIINFLESSFPGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDYEKWREEESHKFTWKQKYYKGLGTSLAQEVREYFSNLDRHLKIFHSLQGNDKDYIDLAFSKKKADDRKEWLRQYEPGTVLDPTLKEIPISDFINKELILFSLADNIRSIPNVLDGFKPGQRKVLYGCFKKNLKSELKVAQLAPYVSECTAYHHGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAFGTRATGGKDAAAARYIYTELNKLTRKIFHPADDPLYKYIQEDEKTVEPEWYLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEELEQMHPWFRGWTGTIEEIEPLRYRMYGRIEQIGDNVLEITELPARTWTSTIKEYLLLGLSGNDKIKPWIKDMEEQHDDNIKFIITLSPEEMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYNSVNEILSEFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKELTVTNKPRNAIIQELENLGFPRFNKEGKPYYGSPNDEIAEQINDVKGATSDEEDEESSHEDTENVINGPEELYGTYEYLLGMRIWSLTKERYQKLLKQKQEKETELENLLKLSAKDIWNTDLKAFEVGYQEFLQRDAEAR 1177
               SCOP domains d2rgra_ A: DNA topoisomerase II, C-terminal fragment (residues 410-1202)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------2rgrA01 A:429-561,A:609-691  [code=3.40.50.670, no name defined]                                                                     2rgrA02 A:562-608                              2rgrA01 A:429-561,A:609-691  [code=3.40.50.670, no name defined]                   2rgrA03 A:692-860,A:974-988 Topoisomerase II, domain 5                                                                                                                   -----------2rgrA04 A:872-973  [code=3.30.1360.40, no name defined]                                               2rgrA03        2rgrA05 A:989-1177 Topoisomerase, domain 3                                                                                                                                                    CATH domains
               Pfam domains -------------------------Toprim-2rgrA01 A:444-554                                                                                       ---------------------------------------------------------------------------------------------------------------------------------------DNA_topoisoIV-2rgrA02 A:690-1160                                                                                                                                                                                                                                                                                                                                                                                                                                                       ----------------- Pfam domains
         Sec.struct. author ....................hhhh.eeeeeehhhhhhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhhhhhhhh................eeeee...hhhhhhhhhhhhhhhhhhh.hhhhh...eeee....eeeee......eeee.hhhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhh...eeee.....hhhhhhhhhhh..hhhhhhhhhhhh...........ee.hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.....eehhhhhhhhhhh.....hhhhhhhhhhhhhh............................hhhh.ee....hhhhhhhhhhhhhh.eeee..eeeee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhh................eeee....eeeee.eeeeee..eeeeee.....hhhhhhhhhhhhhhh.........eeee.......eeee.hhhhhhhhhhhhhhhhh..eeeee...eeee.....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh...ee.....ee...--------------------------------------....hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. 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:419-1177 (gaps) UniProt: 1-1428 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Transcript 1
                2rgr A  419 RKSRITNYPKLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLIINFLESSFLGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDYEKWREEESHKFTWKQKYYKGLGTSLAQEVREYFSNLDRHLKIFHSLQGNDKDYIDLAFSKKKADDRKEWLRQYEPGTVLDPTLKEIPISDFINKELILFSLADNIRSIPNVLDGFKPGQRKVLYGCFKKNLKSELKVAQLAPYVSECTAYHHGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAFGTRATGGKDAAAARYIYTELNKLTRKIFHPADDPLYKYIQEDEKTVEPEWYLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEELEQMHPWFRGWTGTIEEIEPLRYRMYGRIEQIGDNVLEITELPARTWTSTIKEYLLLGLSGNDKIKPWIKDMEEQHDDNIKFIITLSPEEMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYNSVNEILSEFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKELTVTNKPRNAIIQELENLGFPRFNKEGKPYYGS--------------------------------------LYGTYEYLLGMRIWSLTKERYQKLLKQKQEKETELENLLKLSAKDIWNTDLKAFEVGYQEFLQRDAEAR 1177
                                   428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008      1018      1028      1038      1048      1058      1068 |       -         -         -         -|     1118      1128      1138      1148      1158      1168         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    1070                                   1109

Chain C from PDB  Type:DNA  Length:15
                                                
                2rgr C    1 CCGAGGATGACGATG   15
                                    10

Chain D from PDB  Type:DNA  Length:19
                                                    
                2rgr D    1 CGCGCATCGTCATCCTCGG   19
                                    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 '\|'

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
		Arg A:482 - Glu A:483	[ RasMol ]
		Lys A:570 - Pro A:571	[ RasMol ]

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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	2rgr
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	TOP2_YEAST \| P06786
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	5.99.1.3
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	TOP2_YEAST \| P06786	:	1bgw 1bjt 1pvg 1qzr 3l4j 3l4k 4gfh

(no "Related Entries Specified in the PDB File" available for 2RGR)

Description

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Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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