1KZN - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF E. COLI 24KDA DOMAIN IN COMPLEX WITH CLOROBIOCIN

Authors :   D. Lafitte, V. Lamour, P. O. Tsvetkov, A. A. Makarov, M. Klich, P. Deprez, D. Moras, C. Briand, R. Gilli

Date :   07 Feb 02 (Deposition) - 19 Jun 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A

Keywords :   Topoisomerase, Gyrase B, Clorobiocin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Lafitte, V. Lamour, P. O. Tsvetkov, A. A. Makarov, M. Klich, P. Deprez, D. Moras, C. Briand, R. Gilli
Dna Gyrase Interaction With Coumarin-Based Inhibitors: The Role Of The Hydroxybenzoate Isopentenyl Moiety And The 5'-Methyl Group Of The Noviose.
Biochemistry V. 41 7217 2002
PubMed-ID: 12044152 | Reference-DOI: 10.1021/BI0159837
(for further references see the PDB file header)

Molecule 1 - DNA GYRASE SUBUNIT B
	Chains	:	A
	EC Number	:	5.99.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	24 KDA N-TERMINUS DOMAIN
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	GYRASE B

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	CBN	1	Ligand/Ion	CLOROBIOCIN

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:22 , TYR A:26 , ASN A:46 , GLU A:50 , VAL A:71 , ASP A:73 , ARG A:76 , GLY A:77 , ILE A:78 , PRO A:79 , ILE A:90 , HIS A:95 , ARG A:136 , THR A:165 , HOH A:1122 , HOH A:1154 , HOH A:1160 , HOH A:1172 , HOH A:1176	BINDING SITE FOR RESIDUE CBN A 1

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

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

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

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

(no "Exon" information available for 1KZN)

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:186
 aligned with GYRB_ECO57 | P0AES7 from UniProtKB/Swiss-Prot  Length:804

    Alignment length:205
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214     
           GYRB_ECO57    15 GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYE 219
               SCOP domains d1kzna_ A: DNA gyrase B                                                                                                                                                                                       SCOP domains
               CATH domains 1kznA00 A:15-219  [code=3.30.565.10, no name defined]                                                                                                                                                         CATH domains
               Pfam domains ----------------HATPase_c-1kznA01 A:31-174                                                                                                                      --------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....eeeeeee...eeeeee.........----..hhhhhhhhh...---------------...hhhhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.....eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kzn A  15 GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGI----GVSAAEVIMTVLHA---------------HGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYE 219
                                    24        34        44        54        64        74       | -  |     90     |   -         - |     124       134       144       154       164       174       184       194       204       214     
                                                                                              82   83           96             116

Chain A from PDB  Type:PROTEIN  Length:186
 aligned with GYRB_ECOLI | P0AES6 from UniProtKB/Swiss-Prot  Length:804

    Alignment length:205
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214     
           GYRB_ECOLI    15 GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYE 219
               SCOP domains d1kzna_ A: DNA gyrase B                                                                                                                                                                                       SCOP domains
               CATH domains 1kznA00 A:15-219  [code=3.30.565.10, no name defined]                                                                                                                                                         CATH domains
               Pfam domains ----------------HATPase_c-1kznA01 A:31-174                                                                                                                      --------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....eeeeeee...eeeeee.........----..hhhhhhhhh...---------------...hhhhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.....eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kzn A  15 GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGI----GVSAAEVIMTVLHA---------------HGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYE 219
                                    24        34        44        54        64        74       | -  |     90     |   -         - |     124       134       144       154       164       174       184       194       204       214     
                                                                                              82   83           96             116

Chain A from PDB  Type:PROTEIN  Length:186
 aligned with GYRB_SHIFL | P0AES8 from UniProtKB/Swiss-Prot  Length:804

    Alignment length:205
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214     
           GYRB_SHIFL    15 GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYE 219
               SCOP domains d1kzna_ A: DNA gyrase B                                                                                                                                                                                       SCOP domains
               CATH domains 1kznA00 A:15-219  [code=3.30.565.10, no name defined]                                                                                                                                                         CATH domains
               Pfam domains ----------------HATPase_c-1kznA01 A:31-174                                                                                                                      --------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....eeeeeee...eeeeee.........----..hhhhhhhhh...---------------...hhhhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.....eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kzn A  15 GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGI----GVSAAEVIMTVLHA---------------HGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYE 219
                                    24        34        44        54        64        74       | -  |     90     |   -         - |     124       134       144       154       164       174       184       194       204       214     
                                                                                              82   83           96             116

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

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. (3)

1kznA00

A:15-219

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: His_Kinase_A (147)

Family: HATPase_c (132)

Escherichia coli O157:H7 (1)

HATPase_c-1kznA01

A:31-174

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (GYRB_ECOLI | P0AES6)

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:0034335	DNA supercoiling activity	Catalytic introduction of supercoils in a DNA molecule or region thereof. In bacteria, negative supercoils are only introduced by DNA gyrase, a type II topoisomerase, but not all DNA gyrases are capable of introducing supercoils. In bacteria, the level of supercoiling varies widely between species and has been characterized properly in only a handful of organisms. The best characterized enzyme, from E.coli, is exceptionally proficient at supercoiling and this ability is not representative of all bacteria.
	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:0008094	DNA-dependent ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of single- or double-stranded DNA, and it drives another reaction.
	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.
	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: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:0006261	DNA-dependent DNA replication	A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.
	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: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:0042493	response to drug	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 a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.

Chain A (GYRB_ECO57 | P0AES7)

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:0006261	DNA-dependent DNA replication	A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.
	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.
cellular component
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A (GYRB_SHIFL | P0AES8)

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:0006261	DNA-dependent DNA replication	A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.
	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.
cellular component
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	1kzn
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	5.99.1.3
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UniProtKB/Swiss-Prot
	GYRB_ECO57 \| P0AES7	:	1aj6 1ei1 4zvi 5mmn 5mmo 5mmp
	GYRB_ECOLI \| P0AES6	:	1aj6 1ei1 3g7e 3nuh 4duh 4hyp 4kfg 4prv 4prx 4pu9 4wub 4wuc 4wud 4xtj 4zvi 5l3j
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(no "Related Entries Specified in the PDB File" available for 1KZN)

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Ligands, Modified Residues, Ions (1, 1)

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