P0A0K8 (GYRB_STAAU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA gyrase subunit B
EC=5.99.1.3

Gene names

Name:

gyrB

Organism

Staphylococcus aureus

Taxonomic identifier

1280 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Staphylococcus

Protein attributes

Sequence length	644 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. HAMAP MF_01898
Catalytic activity	ATP-dependent breakage, passage and rejoining of double-stranded DNA. HAMAP MF_01898
Subunit structure	Made up of two chains. The A chain is responsible for DNA breakage and rejoining; the B chain catalyzes ATP hydrolysis. The enzyme forms an A2B2 tetramer.
Subcellular location	Cytoplasm Potential HAMAP 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 Nucleotide-binding
Molecular function	Isomerase Topoisomerase
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological process	DNA topological change Inferred from electronic annotation. Source: InterPro response to antibiotic Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	chromosome Inferred from electronic annotation. Source: InterPro cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA topoisomerase (ATP-hydrolyzing) activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.1

Chain

2 – 644

643

DNA gyrase subunit B HAMAP MF_01898

PRO_0000145342

Regions

Domain

459 – 540

82

Toprim

Experimental info

Sequence conflict

40 – 49

10

SERGLHHLVW → QRELHISV in AAA73951. Ref.3

Sequence conflict

66

1

Q → K in AAA73951. Ref.3

Sequence conflict

312 – 321

10

KIMKEEKDRL → RYEEEKIA in AAA73951. Ref.3

Sequence conflict

424

1

K → Q in AAA73951. Ref.3

Sequence conflict

522

1

T → I in AAA73951. Ref.3

Sequence conflict

579

1

R → L in AAA73951. Ref.3

Secondary structure

1

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644

Helix Strand Turn

Details...

Turn

26 – 30

5

Helix

45 – 60

16

Beta strand

66 – 71

6

Helix

73 – 75

3

Beta strand

77 – 81

5

Helix

98 – 103

6

Helix

130 – 133

4

Beta strand

135 – 144

10

Beta strand

147 – 153

7

Beta strand

158 – 160

3

Beta strand

174 – 179

6

Helix

192 – 205

14

Beta strand

210 – 215

6

Beta strand

221 – 227

7

Sequences

	Sequence		Length	Mass (Da)
	P0A0K8 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: CED22E8C446A1138	FASTA	644	72,540
	10 20 30 40 50 60 MVTALSDVNN TDNYGAGQIQ VLEGLEAVRK RPGMYIGSTS ERGLHHLVWE IVDNSIDEAL 70 80 90 100 110 120 AGYANQIEVV IEKDNWIKVT DNGRGIPVDI QEKMGRPAVE VILTVLHAGG KFGGGGYKVS 130 140 150 160 170 180 GGLHGVGSSV VNALSQDLEV YVHRNETIYH QAYKKGVPQF DLKEVGTTDK TGTVIRFKAD 190 200 210 220 230 240 GEIFTETTVY NYETLQQRIR ELAFLNKGIQ ITLRDERDEE NVREDSYHYE GGIKSYVELL 250 260 270 280 290 300 NENKEPIHDE PIYIHQSKDD IEVEIAIQYN SGYATNLLTY ANNIHTYEGG THEDGFKRAL 310 320 330 340 350 360 TRVLNSYGLS SKIMKEEKDR LSGEDTREGM TAIISIKHGD PQFEGQTKTK LGNSEVRQVV 370 380 390 400 410 420 DKLFSEHFER FLYENPQVAR TVVEKGIMAA RARVAAKKAR EVTRRKSALD VASLPGKLAD 430 440 450 460 470 480 CSSKSPEECE IFLVEGDSAG GSTKSGRDSR TQAILPLRGK ILNVEKARLD RILNNNEIRQ 490 500 510 520 530 540 MITAFGTGIG GDFDLAKARY HKIVIMTDAD VDGAHIRTLL LTFFYRFMRP LIEAGYVYIA 550 560 570 580 590 600 QPPLYKLTQG KQKYYVYNDR ELDKLKSELN PTPKWSIARY KGLGEMNADQ LWETTMNPEH 610 620 630 640 RALLQVKLED AIEADQTFEM LMGDVVENRR QFIEDNAVYA NLDF

References

[1]	"Cloning, sequencing, and expression of the DNA gyrase genes from Staphylococcus aureus." Brockbank S.M.V., Barth P.T. J. Bacteriol. 175:3269-3277(1993) [PubMed: 8388872] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-27 AND 314-335. Strain: 601055.
[2]	"Quinolone resistance mutations in the DNA gyrase gyrA and gyrB genes of Staphylococcus aureus." Ito H., Yoshida H., Bogaki-Shonai M., Niga T., Hattori H., Nakamura S. Antimicrob. Agents Chemother. 38:2014-2023(1994) [PubMed: 7811012] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 12600 / IAM 12544 / NCTC 8532.
[3]	"Nucleotide sequence of the Staphylococcus aureus gyrB-gyrA locus encoding the DNA gyrase A and B proteins." Margerrison E.E.C., Hopewell R., Fisher L.M. J. Bacteriol. 174:1596-1603(1992) [PubMed: 1311298] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]	"Nucleotide sequence of the recF gene cluster from Staphylococcus aureus and complementation analysis in Bacillus subtilis recF mutants." Alonso J.C., Fisher L.M. Mol. Gen. Genet. 246:680-686(1995) [PubMed: 7898435] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-30. Strain: YB886.
[5]	"DNA cloning and organization of the Staphylococcus aureus gyrA and gyrB genes: close homology among gyrase proteins and implications for 4-quinolone action and resistance." Hopewell R., Oram M., Briesewitz R., Fisher L.M. J. Bacteriol. 172:3481-3484(1990) [PubMed: 2160946] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 593-644.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X71437 Genomic DNA. Translation: CAA50570.1.
D10489 Genomic DNA. Translation: BAA01369.1.
M86227 Genomic DNA. Translation: AAA73951.1.
M37915 Genomic DNA. Translation: AAA26635.1.

PIR

A40585.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3G75	X-ray	2.30	A/B	24-230	[»]
3G7B	X-ray	2.30	A/B	24-230	[»]
3TTZ	X-ray	1.63	A/B	14-233	[»]

ProteinModelPortal

P0A0K8.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

HAMAP

MF_01898. GyrB.
[Tree]

InterPro

IPR003594. ATPase-like_ATP-bd.
IPR011557. GyrB.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
IPR001241. Topo_IIA.
IPR013759. Topo_IIA_B/N_ab.
IPR002288. Topo_IIA_B_C.
IPR013506. Topo_IIA_bsu_dom2.
IPR013760. Topo_IIA_cen.
IPR018522. TopoIIA_CS.
IPR006171. Toprim_domain.
[Graphical view]

Gene3D

G3DSA:3.30.565.10. ATP_bd_ATPase. 1 hit.
G3DSA:3.30.230.10. Ribosomal_S5_D2-type_fold. 1 hit.
G3DSA:3.40.50.670. Topo_IIA_B/N_ab. 1 hit.

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.
[Graphical view]

ProtoNet

Search...

Other

DrugBank

DB01051. Novobiocin.

Entry information

Entry name

GYRB_STAAU

Accession

Primary (citable) accession number: P0A0K8
Secondary accession number(s): P20832

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 15, 2005
Last sequence update:	January 23, 2007
Last modified:	January 25, 2012
This is version 40 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program