1S16 - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF E. COLI TOPOISOMERASE IV PARE 43KDA SUBUNIT COMPLEXED WITH ADPNP

Authors :   Y. Wei, C. H. Gross

Date :   05 Jan 04 (Deposition) - 04 May 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   Two-Domain Protein Complexed With Adpnp, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Bellon, J. D. Parsons, Y. Wei, K. Hayakawa, L. L. Swenson, P. S. Charifson, J. A. Lippke, R. Aldape, C. H. Gross
Crystal Structures Of Escherichia Coli Topoisomerase Iv Par Subunit (24 And 43 Kilodaltons): A Single Residue Dictates Differences In Novobiocin Potency Against Topoisomerase Iv And Dna Gyrase.
Antimicrob. Agents Chemother. V. 48 1856 2004
PubMed-ID: 15105144 | Reference-DOI: 10.1128/AAC.48.5.1856-1864.2004

Molecule 1 - TOPOISOMERASE IV SUBUNIT B
	Chains	:	A, B
	EC Number	:	5.99.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	43KDA SUBUNIT
	Gene	:	PARE, NFXD, B3030
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	ANP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 4)

No.	Name	Count	Type	Full Name
1	ANP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:1090 , ARG A:1093 , ALA A:1096 , GLY A:1113 , SER A:1117 , ANP A:1500	BINDING SITE FOR RESIDUE MG A 1501
2	AC2	SOFTWARE	ILE B:2090 , ARG B:2093 , ALA B:2096 , GLY B:2113 , SER B:2117 , ANP B:2500	BINDING SITE FOR RESIDUE MG B 2501
3	AC3	SOFTWARE	ARG A:1178 , SER A:1180 , VAL A:1181 , SER A:1182 , HOH A:3186	BINDING SITE FOR RESIDUE SO4 A 1502
4	AC4	SOFTWARE	ARG B:2178 , SER B:2180 , VAL B:2181 , SER B:2182 , HOH B:3243	BINDING SITE FOR RESIDUE SO4 B 2502
5	AC5	SOFTWARE	GLU A:1038 , ASN A:1042 , GLU A:1046 , ASP A:1069 , MET A:1074 , ILE A:1090 , ALA A:1096 , GLY A:1097 , GLY A:1098 , LYS A:1099 , TYR A:1105 , GLY A:1110 , LEU A:1111 , HIS A:1112 , GLY A:1113 , VAL A:1114 , GLY A:1115 , ILE A:1116 , THR A:1163 , GLN A:1332 , LYS A:1334 , MG A:1501 , HOH A:3001 , HOH A:3003 , HOH A:3042 , HOH A:3073 , HOH A:3079 , HOH A:3081 , TYR B:2005 , ILE B:2010	BINDING SITE FOR RESIDUE ANP A 1500
6	AC6	SOFTWARE	TYR A:1005 , GLU B:2038 , ASN B:2042 , GLU B:2046 , ASP B:2069 , MET B:2074 , ILE B:2090 , ALA B:2096 , GLY B:2097 , GLY B:2098 , LYS B:2099 , TYR B:2105 , GLY B:2110 , LEU B:2111 , HIS B:2112 , GLY B:2113 , VAL B:2114 , GLY B:2115 , ILE B:2116 , GLN B:2332 , LYS B:2334 , MG B:2501 , HOH B:3002 , HOH B:3008 , HOH B:3030 , HOH B:3072 , HOH B:3093 , HOH B:3183	BINDING SITE FOR RESIDUE ANP B 2500

(no "SS Bond" information available for 1S16)

Asymmetric Unit

No.	Residues
1	Leu A:1233	-	Pro A:1234
2	Leu B:2233	-	Pro B:2234

(no "SAP(SNP)/Variant" information available for 1S16)

(no "PROSITE Motif" information available for 1S16)

(no "Exon" information available for 1S16)

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:380
 aligned with PARE_ECOLI | P20083 from UniProtKB/Swiss-Prot  Length:630

    Alignment length:380
                                    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
          PARE_ECOLI      4 TYNADAIEVLTGLEPVRRRPGMYTDTTRPNHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDDGRGMPVDIHPEEGVPAVELILCRLHAGGKFSNKNYQFSGGLHGVGISVVNALSKRVEVNVRRDGQVYNIAFENGEKVQDLQVVGTCGKRNTGTSVHFWPDETFFDSPRFSVSRLTHVLKAKAVLCPGVEITFKDEINNTEQRWCYQDGLNDYLAEAVNGLPTLPEKPFIGNFAGDTEAVDWALLWLPEGGELLTESYVNLIPTMQGGTHVNGLRQGLLDAMREFCEYRNILPRGVKLSAEDIWDRCAYVLSVKMQDPQFAGQTKERLSSRQCAAFVSGVVKDAFILWLNQNVQAAELLAEMAISSAQRRMRAA  383
               SCOP domains d1s16a2 A:1004-1216 Topoisomerase IV subunit B                                                                                                                                                                       d1s16a1 A:1217-1383 Topoisomerase IV subunit B                                                                                                                          SCOP domains
               CATH domains 1s16A01 A:1004-1215  [code=3.30.565.10, no name defined]                                                                                                                                                            1s16A02 A:1216-1383  [code=3.30.230.10, no name defined]                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhee...hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....eeeeee.....eeeee...............hhhhhhhhh..ee................hhhhhhhhheeeeeeeeee..eeeeeeee..eeeeeeeeeee......eeeeeeee.hhhh.....hhhhhhhhhhhhhhhh...eeeeee....eeeee....hhhhhhhhhhh....eeeeeeeeeee...eeeeeeeee........eeeee..ee....hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhh.eeeeeeeee................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1s16 A 1004 TYNADAIEVLTGLEPVRRRPGMYTDTTRPNHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDDGRGMPVDIHPEEGVPAVELILCRLHAGGKFSNKNYQFSGGLHGVGISVVNALSKRVEVNVRRDGQVYNIAFENGEKVQDLQVVGTCGKRNTGTSVHFWPDETFFDSPRFSVSRLTHVLKAKAVLCPGVEITFKDEINNTEQRWCYQDGLNDYLAEAVNGLPTLPEKPFIGNFAGDTEAVDWALLWLPEGGELLTESYVNLIPTMQGGTHVNGLRQGLLDAMREFCEYRNILPRGVKLSAEDIWDRCAYVLSVKMQDPQFAGQTKERLSSRQCAAFVSGVVKDAFILWLNQNVQAAELLAEMAISSAQRRMRAA 1383
                                  1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263      1273      1283      1293      1303      1313      1323      1333      1343      1353      1363      1373      1383

Chain B from PDB  Type:PROTEIN  Length:380
 aligned with PARE_ECOLI | P20083 from UniProtKB/Swiss-Prot  Length:630

    Alignment length:380
                                    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
          PARE_ECOLI      4 TYNADAIEVLTGLEPVRRRPGMYTDTTRPNHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDDGRGMPVDIHPEEGVPAVELILCRLHAGGKFSNKNYQFSGGLHGVGISVVNALSKRVEVNVRRDGQVYNIAFENGEKVQDLQVVGTCGKRNTGTSVHFWPDETFFDSPRFSVSRLTHVLKAKAVLCPGVEITFKDEINNTEQRWCYQDGLNDYLAEAVNGLPTLPEKPFIGNFAGDTEAVDWALLWLPEGGELLTESYVNLIPTMQGGTHVNGLRQGLLDAMREFCEYRNILPRGVKLSAEDIWDRCAYVLSVKMQDPQFAGQTKERLSSRQCAAFVSGVVKDAFILWLNQNVQAAELLAEMAISSAQRRMRAA  383
               SCOP domains d1s16b2 B:2004-2216 Topoisomerase IV subunit B                                                                                                                                                                       d1s16b1 B:2217-2383 Topoisomerase IV subunit B                                                                                                                          SCOP domains
               CATH domains 1s16B01 B:2004-2215  [code=3.30.565.10, no name defined]                                                                                                                                                            1s16B02 B:2216-2383  [code=3.30.230.10, no name defined]                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhee...hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....eeeeee.....eeeee...............hhhhhhhhh..ee................hhhhhhhhheeeeeeeeee..eeeeeeee..eeeeeeeeeee......eeeeeeee.hhhh.....hhhhhhhhhhhhhhhh...eeeeee....eeeee....hhhhhhhhhh.....eeeeeeeeeee...eeeeeeeee........eeeee..ee....hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhh.eeeeeeeee................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1s16 B 2004 TYNADAIEVLTGLEPVRRRPGMYTDTTRPNHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDDGRGMPVDIHPEEGVPAVELILCRLHAGGKFSNKNYQFSGGLHGVGISVVNALSKRVEVNVRRDGQVYNIAFENGEKVQDLQVVGTCGKRNTGTSVHFWPDETFFDSPRFSVSRLTHVLKAKAVLCPGVEITFKDEINNTEQRWCYQDGLNDYLAEAVNGLPTLPEKPFIGNFAGDTEAVDWALLWLPEGGELLTESYVNLIPTMQGGTHVNGLRQGLLDAMREFCEYRNILPRGVKLSAEDIWDRCAYVLSVKMQDPQFAGQTKERLSSRQCAAFVSGVVKDAFILWLNQNVQAAELLAEMAISSAQRRMRAA 2383
                                  2013      2023      2033      2043      2053      2063      2073      2083      2093      2103      2113      2123      2133      2143      2153      2163      2173      2183      2193      2203      2213      2223      2233      2243      2253      2263      2273      2283      2293      2303      2313      2323      2333      2343      2353      2363      2373      2383

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

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Heat Shock Protein 90 (209)

Homologous Superfamily: [code=3.30.565.10, no name defined] (205)

Escherichia coli. Organism_taxid: 562. (9)

1a	1s16A01	A:1004-1215
1b	1s16B01	B:2004-2215

Topology: Ribosomal Protein S5; domain 2 (189)

Homologous Superfamily: [code=3.30.230.10, no name defined] (170)

Escherichia coli. Organism_taxid: 562. (1)

2a	1s16A02	A:1216-1383
2b	1s16B02	B:2216-2383

(no "Pfam Domain" information available for 1S16)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PARE_ECOLI | P20083)

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: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: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:0051276	chromosome organization	A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome.
	GO:0007059	chromosome segregation	The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
	GO:0030541	plasmid partitioning	Any process in which plasmids are segregated or distributed into daughter cells upon cell division.
	GO:0046677	response to antibiotic	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
	GO:0007062	sister chromatid cohesion	The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other.
cellular component
	GO:0009330	DNA topoisomerase complex (ATP-hydrolyzing)	Complex that possesses DNA topoisomerase (ATP-hydrolyzing) activity.
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0009295	nucleoid	The region of a virus, bacterial cell, mitochondrion or chloroplast to which the nucleic acid is confined.

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	Cis Peptide Bonds
		Leu A:1233 - Pro A:1234	[ RasMol ]
		Leu B:2233 - Pro B:2234	[ RasMol ]

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	1s16
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Ligands, Modified Residues, Ions (3, 6)

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