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Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Chlamydia trachomatis (strain D/UW-3/Cx)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Protein inferred from homologyi

Functioni

A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner.UniRule annotation

Catalytic activityi

ATP-dependent breakage, passage and rejoining of double-stranded DNA.UniRule annotation

Cofactori

Mg2+UniRule annotation, Mn2+UniRule annotation, Ca2+UniRule annotationNote: 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+ or Ca2+.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi437 – 4371Magnesium 1; catalyticUniRule annotation
Metal bindingi511 – 5111Magnesium 1; catalyticUniRule annotation
Metal bindingi511 – 5111Magnesium 2UniRule annotation
Metal bindingi513 – 5131Magnesium 2UniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

ATP-binding, DNA-binding, Magnesium, Metal-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
DNA gyrase subunit BUniRule annotation (EC:5.99.1.3UniRule annotation)
Gene namesi
Name:gyrBUniRule annotation
Ordered Locus Names:CT_190
OrganismiChlamydia trachomatis (strain D/UW-3/Cx)
Taxonomic identifieri272561 [NCBI]
Taxonomic lineageiBacteriaChlamydiaeChlamydialesChlamydiaceaeChlamydia/Chlamydophila groupChlamydia
Proteomesi
  • UP000000431 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 804804DNA gyrase subunit BPRO_0000145305Add
BLAST

Proteomic databases

PRIDEiO84193.

Interactioni

Subunit structurei

Heterotetramer, composed of two GyrA and two GyrB chains. In the heterotetramer, GyrA contains the active site tyrosine that forms a transient covalent intermediate with DNA, while GyrB binds cofactors and catalyzes ATP hydrolysis.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei462 – 4621Interaction with DNAUniRule annotation
Sitei465 – 4651Interaction with DNAUniRule annotation

Protein-protein interaction databases

STRINGi272561.CT190.

Structurei

3D structure databases

ProteinModelPortaliO84193.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini431 – 546116ToprimUniRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the type II topoisomerase GyrB family.UniRule annotation
Contains 1 Toprim domain.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C7D. Bacteria.
COG0187. LUCA.
InParanoidiO84193.
KOiK02470.
OMAiIKNMITA.
OrthoDBiEOG6P334W.

Family and domain databases

Gene3Di3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 2 hits.
HAMAPiMF_01898. GyrB.
InterProiIPR002288. DNA_gyrase_B_C.
IPR011557. GyrB.
IPR003594. HATPase_C.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
IPR001241. Topo_IIA.
IPR013760. Topo_IIA-like_dom.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR018522. TopoIIA_CS.
IPR006171. Toprim_domain.
[Graphical view]
PfamiPF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSiPR00418. TPI2FAMILY.
SMARTiSM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 2 hits.
TIGRFAMsiTIGR01059. gyrB. 1 hit.
PROSITEiPS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O84193-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDAQEKKYDA SAITVLEGLQ AVRERPGMYI GDTGVTGLHH LVYEVVDNSI
60 70 80 90 100
DEAMAGFCTE VVVRILEDGG ISISDNGRGI PIQIHEKESA KQGREISALE
110 120 130 140 150
VVLTVLHAGG KFDKDSYKVS GGLHGVGVSC VNALSEKFIA KVFKDGQAYS
160 170 180 190 200
MEFSRGAPLT TLQVLGPTDK RGTEVLFYPD PAIFSTCVFD RAILMKRLRE
210 220 230 240 250
LAFLNRGVTI VFEDDRDTGF DKVVFFYEGG IQSFVSYLNQ NKEILFPNPI
260 270 280 290 300
YMQGSRPGDD GDIEFEAALQ WNSGYSELIY SYANNIPTRQ GGTHLTGFST
310 320 330 340 350
ALTRAVNSYI KAHNLSKSDK LSLTGEDIKE GLVAIVSVKV PNPQFEGQTK
360 370 380 390 400
QKLGNSDVGS VSQQISGEVL TTFFEENPQI AKTIVDKVFV AAQAREAAKR
410 420 430 440 450
ARELTLRKSA LDSARLPGKL IDCLEKDPEK CEMYIVEGDS AGGSAKQGRD
460 470 480 490 500
RRFQAILPIR GKILNVEKAR LQKVFQNQEI GSIIAALGCG IGKDNFNLSK
510 520 530 540 550
LRYKRIIIMT DADVDGSHIR TLLLTFFYRH MSALIENECV YIAQPPLYRV
560 570 580 590 600
SKKKDFRYIL SEKEMDGYLL NLGTKESQIV FDDTLRDLRG EALETFVNLI
610 620 630 640 650
LEVESFIVSL EKKAIPFSEF LDMFRDGAYP LYYYPPESGK QGGSYLYSHE
660 670 680 690 700
EKEAAIAANE ESASRILELY KGSVLEELQR DLGDYGYDIR NYLHPKGSGI
710 720 730 740 750
TVSTEDPKIS PYVCYTLKEV IDYLKGLGRK GIEIQRYKGL GEMNADQLWD
760 770 780 790 800
TTMNPEQRTL VRVSLKDAVE ADHIFTMLMG EEVPPRREFI ESHALSIRMN

NLDI
Length:804
Mass (Da):89,774
Last modified:November 1, 1998 - v1
Checksum:i3DE9305D78936A2A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE001273 Genomic DNA. Translation: AAC67782.1.
PIRiG71546.
RefSeqiNP_219694.1. NC_000117.1.
WP_009871536.1. NC_000117.1.

Genome annotation databases

EnsemblBacteriaiAAC67782; AAC67782; CT_190.
GeneIDi884937.
KEGGictr:CT_190.
PATRICi20379883. VBIChlTra43535_0204.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE001273 Genomic DNA. Translation: AAC67782.1.
PIRiG71546.
RefSeqiNP_219694.1. NC_000117.1.
WP_009871536.1. NC_000117.1.

3D structure databases

ProteinModelPortaliO84193.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi272561.CT190.

Proteomic databases

PRIDEiO84193.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC67782; AAC67782; CT_190.
GeneIDi884937.
KEGGictr:CT_190.
PATRICi20379883. VBIChlTra43535_0204.

Phylogenomic databases

eggNOGiENOG4105C7D. Bacteria.
COG0187. LUCA.
InParanoidiO84193.
KOiK02470.
OMAiIKNMITA.
OrthoDBiEOG6P334W.

Family and domain databases

Gene3Di3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 2 hits.
HAMAPiMF_01898. GyrB.
InterProiIPR002288. DNA_gyrase_B_C.
IPR011557. GyrB.
IPR003594. HATPase_C.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
IPR001241. Topo_IIA.
IPR013760. Topo_IIA-like_dom.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR018522. TopoIIA_CS.
IPR006171. Toprim_domain.
[Graphical view]
PfamiPF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSiPR00418. TPI2FAMILY.
SMARTiSM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 2 hits.
TIGRFAMsiTIGR01059. gyrB. 1 hit.
PROSITEiPS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis."
    Stephens R.S., Kalman S., Lammel C.J., Fan J., Marathe R., Aravind L., Mitchell W.P., Olinger L., Tatusov R.L., Zhao Q., Koonin E.V., Davis R.W.
    Science 282:754-759(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: D/UW-3/Cx.

Entry informationi

Entry nameiGYRB_CHLTR
AccessioniPrimary (citable) accession number: O84193
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: November 1, 1998
Last modified: June 8, 2016
This is version 100 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Few gyrases are as efficient as E.coli at forming negative supercoils. Not all organisms have 2 type II topoisomerases; in organisms with a single type II topoisomerase this enzyme also has to decatenate newly replicated chromosomes.UniRule annotation

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.