P0AES6 (GYRB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA gyrase subunit B
EC=5.99.1.3

Gene names

Name:	gyrB
Synonyms:	acrB, himB, hisU, nalC, parA, pcbA
Ordered Locus Names:	b3699, JW5625

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	804 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings. Ref.13 Ref.14 Ref.15
Catalytic activity	ATP-dependent breakage, passage and rejoining of double-stranded DNA. Ref.13 Ref.14 Ref.15 Ref.16
Cofactor	Magnesium. Binds two Mg2+ per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn2+ and Ca2+. Ref.13 Ref.14
Enzyme regulation	Target of two classes of inhibitors, coumarins and quinolones. Coumarins bind to GyrB and are competitive inhibitors with respect to ATP. Quinolones bind DNA gyrase when the enzyme is complexed with DNA and trap the enzyme in a covalent reaction intermediate with DNA. HAMAP-Rule MF_01898
Subunit structure	Heterotetramer, composed of two GyrA and two GyrB chains. Within the heterotetramer, GyrA contains the active site tyrosine that forms a covalent intermediate with the DNA, while GyrB contributes the cofactor binding sites and catalyzes ATP hydrolysis. Ref.13 Ref.14 Ref.15
Subcellular location	Cytoplasm Potential HAMAP-Rule MF_01898.
Sequence similarities	Belongs to the type II topoisomerase family. Contains 1 Toprim domain.

Ontologies

Keywords
Biological process	Antibiotic resistance
Cellular component	Cytoplasm
Ligand	ATP-binding DNA-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Isomerase Topoisomerase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	DNA topological change Inferred from mutant phenotype PubMed 6327603. Source: EcoliWiki DNA-dependent DNA replication Inferred from electronic annotation. Source: HAMAP chromosome segregation Inferred from Biological aspect of Ancestor. Source: RefGenome response to antibiotic Inferred from electronic annotation. Source: UniProtKB-KW response to drug Inferred from direct assay PubMed 9144789. Source: EcoliWiki transcription, DNA-dependent Inferred from mutant phenotype PubMed 15535863. Source: EcoliWiki
Cellular_component	DNA topoisomerase complex (ATP-hydrolyzing) Inferred from direct assay PubMed 347446. Source: EcoliWiki chromosome Inferred from electronic annotation. Source: InterPro cytoplasm Inferred from direct assay PubMed 7952188. Source: EcoliWiki nucleoid Inferred from Biological aspect of Ancestor. Source: RefGenome
Molecular_function	ATP binding Inferred from direct assay PubMed 9756859. Source: EcoliWiki DNA topoisomerase type II (ATP-hydrolyzing) activity Inferred from direct assay PubMed 368801. Source: EcoliWiki metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
gyrA	P0AES4	5	EBI-541911,EBI-547129

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed HAMAP-Rule MF_01898

Chain

2 – 804

803

DNA gyrase subunit B HAMAP-Rule MF_01898

PRO_0000145309

Regions

Domain

418 – 533

116

Toprim

Sites

Metal binding

424

1

Magnesium 1; catalytic By similarity

Metal binding

498

1

Magnesium 1; catalytic By similarity

Metal binding

498

1

Magnesium 2 By similarity

Metal binding

500

1

Magnesium 2 By similarity

Site

449

1

Interaction with DNA By similarity

Site

452

1

Interaction with DNA By similarity

Natural variations

Natural variant

426

1

D → N in nal-24, nal-102, nal-103, nal-107, nal-108, nal-111, nal-114, en-2 and en-5 mutants; resistant to nalidixic acid and to enoxacin.

Natural variant

447

1

K → E in nal-31, nal-109, nal-115 and nal-120 mutants; resistant to nalidixic acid.

Natural variant

751

1

W → R in B17 resistant mutant.

Natural variant

759 – 760

2

SR → RC in acriflavine susceptible mutant.

Experimental info

Mutagenesis

424

1

E → A or Q: Strongly reduced activity regarding both DNA supercoiling and relaxation. Reduces ATP hydrolysis in response to DNA binding, but has only minor effect on the basal rate of ATP hydrolysis. Ref.13

Mutagenesis

498

1

D → A or N: Strongly reduced activity regarding both DNA supercoiling and relaxation. Reduces ATP hydrolysis in response to DNA binding, but has only minor effect on the basal rate of ATP hydrolysis. Ref.13

Mutagenesis

500

1

D → A: Strongly reduced activity regarding both DNA supercoiling and relaxation. Reduces ATP hydrolysis in response to DNA binding, but has only minor effect on the basal rate of ATP hydrolysis. Ref.13

Mutagenesis

502

1

D → A: Strongly reduced activity regarding both DNA supercoiling and relaxation. Reduces ATP hydrolysis in response to DNA binding, but has only minor effect on the basal rate of ATP hydrolysis. Ref.13

Sequence conflict

385

1

A → P in AAA62050. Ref.4

Sequence conflict

436

1

R → G in BAA20341. Ref.3

Secondary structure

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804

Helix Strand Turn

Details...

Helix

16 – 21

6

Helix

24 – 27

4

Beta strand

30 – 33

4

Helix

34 – 53

20

Beta strand

58 – 63

6

Turn

65 – 67

3

Beta strand

69 – 73

5

Beta strand

81 – 83

3

Turn

84 – 87

4

Helix

90 – 96

7

Turn

98 – 101

4

Beta strand

102 – 104

3

Beta strand

110 – 112

3

Beta strand

113 – 115

3

Helix

120 – 125

6

Beta strand

127 – 136

10

Beta strand

139 – 146

8

Beta strand

149 – 153

5

Beta strand

155 – 159

5

Beta strand

164 – 171

8

Turn

173 – 175

3

Helix

184 – 197

14

Turn

198 – 200

3

Beta strand

201 – 207

7

Turn

208 – 210

3

Beta strand

213 – 216

4

Beta strand

419 – 424

6

Helix

425 – 435

11

Turn

438 – 440

3

Beta strand

441 – 446

6

Helix

465 – 474

10

Beta strand

491 – 495

5

Turn

501 – 504

4

Helix

505 – 517

13

Helix

519 – 523

5

Beta strand

527 – 530

4

Beta strand

534 – 539

6

Beta strand

542 – 546

5

Helix

549 – 561

13

Beta strand

564 – 571

8

Beta strand

573 – 576

4

Helix

577 – 596

20

Turn

597 – 600

4

Helix

603 – 611

9

Helix

617 – 621

5

Helix

623 – 640

18

Beta strand

646 – 653

8

Beta strand

660 – 667

8

Beta strand

669 – 676

8

Helix

679 – 683

5

Helix

685 – 699

15

Turn

700 – 703

4

Beta strand

704 – 711

8

Beta strand

713 – 718

6

Helix

719 – 730

12

Turn

731 – 733

3

Beta strand

735 – 738

4

Helix

742 – 744

3

Helix

747 – 754

8

Turn

757 – 759

3

Beta strand

762 – 764

3

Helix

767 – 780

14

Sequences

	Sequence		Length	Mass (Da)
	P0AES6 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: D831B95FFB3A7EE3	FASTA	804	89,950
	10 20 30 40 50 60 MSNSYDSSSI KVLKGLDAVR KRPGMYIGDT DDGTGLHHMV FEVVDNAIDE ALAGHCKEII 70 80 90 100 110 120 VTIHADNSVS VQDDGRGIPT GIHPEEGVSA AEVIMTVLHA GGKFDDNSYK VSGGLHGVGV 130 140 150 160 170 180 SVVNALSQKL ELVIQREGKI HRQIYEHGVP QAPLAVTGET EKTGTMVRFW PSLETFTNVT 190 200 210 220 230 240 EFEYEILAKR LRELSFLNSG VSIRLRDKRD GKEDHFHYEG GIKAFVEYLN KNKTPIHPNI 250 260 270 280 290 300 FYFSTEKDGI GVEVALQWND GFQENIYCFT NNIPQRDGGT HLAGFRAAMT RTLNAYMDKE 310 320 330 340 350 360 GYSKKAKVSA TGDDAREGLI AVVSVKVPDP KFSSQTKDKL VSSEVKSAVE QQMNELLAEY 370 380 390 400 410 420 LLENPTDAKI VVGKIIDAAR AREAARRARE MTRRKGALDL AGLPGKLADC QERDPALSEL 430 440 450 460 470 480 YLVEGDSAGG SAKQGRNRKN QAILPLKGKI LNVEKARFDK MLSSQEVATL ITALGCGIGR 490 500 510 520 530 540 DEYNPDKLRY HSIIIMTDAD VDGSHIRTLL LTFFYRQMPE IVERGHVYIA QPPLYKVKKG 550 560 570 580 590 600 KQEQYIKDDE AMDQYQISIA LDGATLHTNA SAPALAGEAL EKLVSEYNAT QKMINRMERR 610 620 630 640 650 660 YPKAMLKELI YQPTLTEADL SDEQTVTRWV NALVSELNDK EQHGSQWKFD VHTNAEQNLF 670 680 690 700 710 720 EPIVRVRTHG VDTDYPLDHE FITGGEYRRI CTLGEKLRGL LEEDAFIERG ERRQPVASFE 730 740 750 760 770 780 QALDWLVKES RRGLSIQRYK GLGEMNPEQL WETTMDPESR RMLRVTVKDA IAADQLFTTL 790 800 MGDAVEPRRA FIEENALKAA NIDI

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nalidixic acid-resistant mutations of the gyrB gene of Escherichia coli." Yamagishi J., Yoshida H., Yamayoshi M., Nakamura S. Mol. Gen. Genet. 204:367-373(1986) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"DNA sequence of the E. coli gyrB gene: application of a new sequencing strategy." Adachi T., Mizuuchi M., Robinson E.A., Appella E., O'Dea M.H., Gellert M., Mizuuchi K. Nucleic Acids Res. 15:771-784(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[3]	"acrB mutation located at carboxyl-terminal region of gyrase B subunit reduces DNA binding of DNA gyrase." Funatsuki K., Tanaka R., Inagaki S., Konno H., Katoh K., Nakamura H. J. Biol. Chem. 272:13302-13308(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12 / N2879.
[4]	"DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication." Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R. Genomics 16:551-561(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[5]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[6]	"Escherichia coli K-12: a cooperatively developed annotation snapshot -- 2005." Riley M., Abe T., Arnaud M.B., Berlyn M.K.B., Blattner F.R., Chaudhuri R.R., Glasner J.D., Horiuchi T., Keseler I.M., Kosuge T., Mori H., Perna N.T., Plunkett G. III, Rudd K.E., Serres M.H., Thomas G.H., Thomson N.R., Wishart D., Wanner B.L. Nucleic Acids Res. 34:1-9(2006) [PubMed] [Europe PMC] [Abstract] Cited for: SEQUENCE REVISION TO 385.
[7]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[8]	"DNA sequence and transcription of the region upstream of the E. coli gyrB gene." Adachi T., Mizuuchi K., Menzel R., Gellert M. Nucleic Acids Res. 12:6389-6395(1984) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-106. Strain: K12.
[9]	"Fusions of the Escherichia coli gyrA and gyrB control regions to the galactokinase gene are inducible by coumermycin treatment." Menzel R., Gellert M. J. Bacteriol. 169:1272-1278(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-22.
[10]	"Characterization of the ATP binding site on Escherichia coli DNA gyrase. Affinity labeling of Lys-103 and Lys-110 of the B subunit by pyridoxal 5'-diphospho-5'-adenosine." Tamura J.K., Gellert M. J. Biol. Chem. 265:21342-21349(1990) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 93-129.
[11]	"The peptide antibiotic microcin B17 induces double-strand cleavage of DNA mediated by E. coli DNA gyrase." Vizan J.L., Hernandez-Chico C., del Castillo I., Moreno F. EMBO J. 10:467-476(1991) [PubMed] [Europe PMC] [Abstract] Cited for: MUTANTS B17 RESISTANT.
[12]	"Escherichia coli proteome analysis using the gene-protein database." VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C. Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY 2D-GEL.
[13]	"The role of GyrB in the DNA cleavage-religation reaction of DNA gyrase: a proposed two metal-ion mechanism." Noble C.G., Maxwell A. J. Mol. Biol. 318:361-371(2002) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBUNIT, MUTAGENESIS OF GLU-424; ASP-498; ASP-500 AND ASP-502.
[14]	"DNA gyrase requires DNA for effective two-site coordination of divalent metal ions: further insight into the mechanism of enzyme action." Sissi C., Chemello A., Vazquez E., Mitchenall L.A., Maxwell A., Palumbo M. Biochemistry 47:8538-8545(2008) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBUNIT.
[15]	"A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function." Schoeffler A.J., May A.P., Berger J.M. Nucleic Acids Res. 38:7830-7844(2010) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF 388-804, SUBUNIT, CATALYTIC ACTIVITY, FUNCTION.
[16]	"Structure-based discovery of substituted 4,5'-bithiazoles as novel DNA gyrase inhibitors." Brvar M., Perdih A., Renko M., Anderluh G., Turk D., Solmajer T. J. Med. Chem. 55:6413-6426(2012) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF 1-220, CATALYTIC ACTIVITY.
[17]	"Quinolone resistance-determining region in the DNA gyrase gyrB gene of Escherichia coli." Yoshida H., Bogaki M., Nakamura M., Yamanaka L.M., Nakamura S. Antimicrob. Agents Chemother. 35:1647-1650(1991) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANTS QUINOLONE-RESISTANT. Strain: K16.
[18]	"Crystal structure of an N-terminal fragment of the DNA gyrase B protein." Wigley D.B., Davies G.J., Dodson E.J., Maxwell A., Dodson G. Nature 351:624-629(1991) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 1-393.
[19]	"The entropic penalty of ordered water accounts for weaker binding of the antibiotic novobiocin to a resistant mutant of DNA gyrase: a thermodynamic and crystallographic study." Holdgate G.A., Tunnicliffe A., Ward W.H., Weston S.A., Rosenbrock G., Barth P.T., Taylor I.W., Pauptit R.A., Timms D. Biochemistry 36:9663-9673(1997) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 1-221 OF MUTANT HIS-136.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X04341 Genomic DNA. Translation: CAA27871.1.
D87842 Genomic DNA. Translation: BAA20341.1.
L10328 Genomic DNA. Translation: AAA62050.1.
U00096 Genomic DNA. Translation: AAT48201.1.
AP009048 Genomic DNA. Translation: BAE77595.1.
M15548 Genomic DNA. Translation: AAA23949.1.

PIR

ISECTB. D65172.

RefSeq

YP_026241.1. NC_000913.2.
YP_491736.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1AJ6	X-ray	2.30	A	2-220	[»]
1EI1	X-ray	2.30	A/B	2-392	[»]
1KZN	X-ray	2.30	A	15-219	[»]
3G7E	X-ray	2.20	A	15-217	[»]
3NUH	X-ray	3.10	B	388-804	[»]
4DUH	X-ray	1.50	A/B	1-220	[»]
4HYP	X-ray	2.60	A/B/C/D	15-220	[»]

ProteinModelPortal

P0AES6.

SMR

P0AES6. Positions 10-392, 402-784.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-48005N.

IntAct

P0AES6. 18 interactions.

STRING

511145.b3699.

Proteomic databases

PaxDb

P0AES6.

PRIDE

P0AES6.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAT48201; AAT48201; b3699.
BAE77595; BAE77595; BAE77595.

GeneID

12930543.
948211.

KEGG

ecj:Y75_p3474.
eco:b3699.

PATRIC

32122895. VBIEscCol129921_3823.

Organism-specific databases

EchoBASE

EB0419.

EcoGene

EG10424. gyrB.

Phylogenomic databases

eggNOG

COG0187.

HOGENOM

HOG000075155.

KO

K02470.

OMA

IFETTEF.

ProtClustDB

PRK14939.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10424-MONOMER.
ECOL316407:JW5625-MONOMER.
MetaCyc:EG10424-MONOMER.

Gene expression databases

Genevestigator

P0AES6.

Family and domain databases

Gene3D

3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 2 hits.

HAMAP

MF_01898. GyrB.

InterPro

IPR002288. DNA_gyrase_B_C.
IPR011557. GyrB.
IPR003594. HATPase_ATP-bd.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
IPR001241. Topo_IIA.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR013760. Topo_IIA_like_dom.
IPR018522. TopoIIA_CS.
IPR006171. Toprim_domain.
[Graphical view]

Pfam

PF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]

PRINTS

PR00418. TPI2FAMILY.

SMART

SM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view]

SUPFAM

SSF55874. ATP_bd_ATPase. 1 hit.
SSF54211. Ribosomal_S5_D2-typ_fold. 1 hit.
SSF56719. Topo_IIA_cen. 1 hit.

TIGRFAMs

TIGR01059. gyrB. 1 hit.

PROSITE

PS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

BindingDB

P0AES6.

ChEMBL

CHEMBL1826.

DrugBank

DB00817. Rosoxacin.

EvolutionaryTrace

P0AES6.

Entry information

Entry name

GYRB_ECOLI

Accession

Primary (citable) accession number: P0AES6
Secondary accession number(s): O08438, P06982, Q2M811

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1988
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 78 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program