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Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
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

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

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)DescriptionActionsGraphical viewLength
Metal bindingi425Magnesium 1; catalyticUniRule annotation1
Metal bindingi499Magnesium 1; catalyticUniRule annotation1
Metal bindingi499Magnesium 2UniRule annotation1
Metal bindingi501Magnesium 2UniRule annotation1

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • DNA binding Source: UniProtKB-KW
  • DNA topoisomerase activity Source: TIGR
  • DNA topoisomerase type II (ATP-hydrolyzing) activity Source: TIGR
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

  • chromosome segregation Source: GO_Central
  • DNA topological change Source: TIGR

Keywordsi

Molecular functionDNA-binding, Isomerase, Topoisomerase
LigandATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciVCHO:VC0015-MONOMER.

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:VC_0015
OrganismiVibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Taxonomic identifieri243277 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
Proteomesi
  • UP000000584 Componenti: Chromosome 1

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

  • chromosome Source: InterPro
  • cytoplasm Source: UniProtKB-SubCell
  • DNA topoisomerase complex (ATP-hydrolyzing) Source: TIGR
  • nucleoid Source: GO_Central

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001453581 – 805DNA gyrase subunit BAdd BLAST805

Proteomic databases

PRIDEiQ9KVX3.

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)DescriptionActionsGraphical viewLength
Sitei450Interaction with DNAUniRule annotation1
Sitei453Interaction with DNAUniRule annotation1

Protein-protein interaction databases

STRINGi243277.VC0015.

Structurei

3D structure databases

ProteinModelPortaliQ9KVX3.
SMRiQ9KVX3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini419 – 534ToprimUniRule annotationAdd BLAST116

Sequence similaritiesi

Belongs to the type II topoisomerase GyrB family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C7D. Bacteria.
COG0187. LUCA.
KOiK02470.
OMAiDCSSRDP.

Family and domain databases

CDDicd03366. TOPRIM_TopoIIA_GyrB. 1 hit.
Gene3Di3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 1 hit.
HAMAPiMF_01898. GyrB. 1 hit.
InterProiView protein in InterPro
IPR002288. 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.
IPR034160. TOPRIM_GyrB.
PANTHERiPTHR10169. PTHR10169. 1 hit.
PfamiView protein in Pfam
PF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
PRINTSiPR00418. TPI2FAMILY.
SMARTiView protein in SMART
SM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 2 hits.
TIGRFAMsiTIGR01059. gyrB. 1 hit.
PROSITEiView protein in PROSITE
PS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.

Sequencei

Sequence statusi: Complete.

Q9KVX3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSNNYDSSSI KVLKGLDAVR KRPGMYIGDT DDGTGLHHMV FEVVDNSIDE
60 70 80 90 100
ALAGYCKDIV VTIHEDNSVS VSDDGRGIPT EMHPEEKVSA AEVIMTVLHA
110 120 130 140 150
GGKFDDNSYK VSGGLHGVGV SVVNALSEKV LLTIYRGGKI HSQTYHHGVP
160 170 180 190 200
QAPLAVVGET ERTGTTVRFW PSAQTFTNIE FHYDILAKRL RELSFLNSGV
210 220 230 240 250
SIKLTDEREE DKKDHFMYEG GIQAFVTHLN RNKTPIHEKV FHFNQEREDG
260 270 280 290 300
ISVEVAMQWN DGFQENIYCF TNNIPQRDGG THLAGFRGAL TRTLNNYMDK
310 320 330 340 350
EGFSKKAQAA TSGDDAREGL TAVVSVKVPD PKFSSQTKDK LVSSEVKSAV
360 370 380 390 400
ESAMNEKLAD FLAENPSEAK NVCSKIIDAA RAREAARKAR EMTRRKGALD
410 420 430 440 450
LAGLPGKLAD CQEKDPALSE LYIVEGDSAG GSAKQGRNRK NQAILPLKGK
460 470 480 490 500
ILNVEKARFD KMLSSQEVAT LITALGCGIG RDEYNPDKLR YHNIIIMTDA
510 520 530 540 550
DVDGSHIRTL LLTFFYRQMP ELIERGYIYI AQPPLYKVKK GKQEQYIKDE
560 570 580 590 600
EAMNQYQVAL AMDGAELHVN ADAPALAGEP LEKLVQQYNA AIKLVERMSR
610 620 630 640 650
RYPYAMLHEL IYVPRINAEL CADKAAVEAW TQRLVEQLNA KEVGASQYSV
660 670 680 690 700
LVEHNAELNV YLPKIQVRTH GVTHEYLLSA DLINSKEYAK LADLSEALDG
710 720 730 740 750
LIEAGAFIKR GERVQPISSF AAALDWLIKE SRRGLSIQRY KGLGEMNPDQ
760 770 780 790 800
LWETTMDPET RRMMQVTIED AVGADELFTT LMGDQVEPRR AFIETNALKV

ANLDV
Length:805
Mass (Da):89,519
Last modified:October 1, 2000 - v1
Checksum:i97F89F4E266D8B45
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE003852 Genomic DNA. Translation: AAF93193.1.
PIRiH82376.
RefSeqiNP_229675.2. NC_002505.1.
WP_000070020.1. NC_002505.1.

Genome annotation databases

EnsemblBacteriaiAAF93193; AAF93193; VC_0015.
GeneIDi2615137.
KEGGivch:VC0015.
PATRICifig|243277.26.peg.14.

Similar proteinsi

Entry informationi

Entry nameiGYRB_VIBCH
AccessioniPrimary (citable) accession number: Q9KVX3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: October 1, 2000
Last modified: June 7, 2017
This is version 108 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families