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Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner (PubMed:23804759, PubMed:11850422). It probably also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes (PubMed:11850422). Relaxes negatively supercoiled DNA in an ATP-independent manner (PubMed:23804759, PubMed:11850422). At comparable concentrations T.thermophilus gyrase does not introduce as many negative supercoils into DNA as the E.coli enzyme (PubMed:23804759).1 Publication
Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner.

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

Temperature dependencei

Optimum temperature is 65 degrees Celsius (PubMed:23804759, PubMed:11850422). Active between 25 and 77 degrees Celsius (PubMed:11850422).2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi422Magnesium 1; catalyticUniRule annotation1
Metal bindingi499Magnesium 1; catalyticUniRule annotation1
Metal bindingi499Magnesium 2UniRule annotation1
Metal bindingi501Magnesium 2UniRule annotation1

GO - Molecular functioni

  • ATP binding Source: UniProtKB-HAMAP
  • DNA binding Source: UniProtKB-HAMAP
  • DNA supercoiling activity Source: UniProtKB
  • magnesium ion binding Source: UniProtKB-HAMAP

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:TTHA1586
OrganismiThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Taxonomic identifieri300852 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
Proteomesi
  • UP000000532 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004355431 – 634DNA gyrase subunit BAdd BLAST634

Interactioni

Subunit structurei

Heterotetramer, composed of two GyrA and two GyrB chains (PubMed:23804759). Non-hydrolyzable ATP analogs induce dimerization, novobiocin also induces a small amount of dimerization (PubMed:11850422). The two subunits form an intertwined dimer where the GyrB ATPase transducer helix of 1 subunit connects to the Toprim domain of the other GyrB subunit through a 10 residue linker (PubMed:23804759). In the heterotetramer, GyrA contains the active site tyrosine that forms a covalent intermediate with the DNA, while GyrB binds cofactors and catalyzes ATP hydrolysis.1 Publication1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei447Interaction with DNAUniRule annotation1
Sitei450Interaction with DNAUniRule annotation1

Protein-protein interaction databases

STRINGi300852.TTHA1586.

Structurei

Secondary structure

1634
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi15 – 19Combined sources5
Helixi22 – 25Combined sources4
Helixi30 – 49Combined sources20
Beta strandi55 – 60Combined sources6
Beta strandi66 – 70Combined sources5
Turni81 – 83Combined sources3
Beta strandi84 – 86Combined sources3
Helixi87 – 93Combined sources7
Beta strandi97 – 99Combined sources3
Helixi100 – 103Combined sources4
Helixi117 – 122Combined sources6
Beta strandi124 – 133Combined sources10
Beta strandi136 – 143Combined sources8
Beta strandi146 – 156Combined sources11
Helixi158 – 160Combined sources3
Beta strandi163 – 170Combined sources8
Helixi172 – 175Combined sources4
Helixi182 – 195Combined sources14
Turni196 – 198Combined sources3
Beta strandi200 – 205Combined sources6
Helixi206 – 208Combined sources3
Beta strandi210 – 214Combined sources5
Helixi219 – 227Combined sources9
Turni228 – 230Combined sources3
Beta strandi239 – 245Combined sources7
Beta strandi248 – 260Combined sources13
Beta strandi263 – 268Combined sources6
Helixi278 – 297Combined sources20
Beta strandi303 – 305Combined sources3
Turni310 – 316Combined sources7
Beta strandi317 – 324Combined sources8
Helixi341 – 361Combined sources21
Helixi363 – 389Combined sources27

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1KIJX-ray2.30A/B1-390[»]
ProteinModelPortaliQ5SHZ4.
SMRiQ5SHZ4.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9LCX5.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini416 – 534ToprimUniRule annotationAdd BLAST119

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 220ATPase domain1 PublicationAdd BLAST220
Regioni221 – 390Transducer domain1 PublicationAdd BLAST170

Domaini

Consists of 3 domains; the ATPase domain (residues 1-220), the transducer domain (221-390) and the toprim domain (391-634) (PubMed:11850422). Removal of the N-terminal ATPase domain (residues 2-392) increases ATP-independent DNA relaxation, showing it is not required for DNA binding or cleavage, this enzyme still has some supercoiling activity, but in this case it introduces positive supercoils (PubMed:23804759).1 Publication1 Publication

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105C7D. Bacteria.
COG0187. LUCA.
HOGENOMiHOG000075156.
KOiK02470.
OMAiIKNMITA.
PhylomeDBiQ5SHZ4.

Family and domain databases

Gene3Di3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 1 hit.
HAMAPiMF_01898. GyrB. 1 hit.
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. 1 hit.
TIGRFAMsiTIGR01059. gyrB. 1 hit.
PROSITEiPS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q5SHZ4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSYDASAIRV LKGLEGVRHR PAMYIGGTGV EGYHHLFKEI LDNAVDEALA
60 70 80 90 100
GYATEILVRL NEDGSLTVED NGRGIPVDLM PEEGKPAVEV IYTTLHSGGK
110 120 130 140 150
FEQGAYKVSG GLHGVGASVV NALSEWTVVE VFREGKHHRI AFSRGEVTEP
160 170 180 190 200
LRVVGEAPRG KTGTRVTFKP DPEIFGNLRF DPSKIRARLR EVAYLVAGLK
210 220 230 240 250
LVFQDRQHGK EEVFLDKGGV ASFAKALAEG EDLLYEKPFL IRGTHGEVEV
260 270 280 290 300
EVGFLHTQGY NAEILTYANM IPTRDGGTHL TAFKSAYSRA LNQYAKKAGL
310 320 330 340 350
NKEKGPQPTG DDLLEGLYAV VSVKLPNPQF EGQTKGKLLN PEAGTAVGQV
360 370 380 390 400
VYERLLEILE ENPRIAKAVY EKALRAAQAR EAARKARELV RRQNPLESDE
410 420 430 440 450
LPGKLADCQT ENPEEAELFI VEGDSAGGSA KQGRDRRFQA ILPLRGKILN
460 470 480 490 500
VEKAGLSKAL KNAEVRAMVS AIGVGIGGDG EAHFDLEGLR YHKIIIMTDA
510 520 530 540 550
DVDGSHIRTL LLTFFYRYMR PLIERGHVYI AQPPLYRLQV GKKVEYLYSD
560 570 580 590 600
EELQARLKEL EGKHYEVQRF KGLGEMNPEQ LWETTMNPEK RVLKRVELQD
610 620 630
ALEASELFEK LMGQEVAPRR EFIEEHARYA ELDI
Length:634
Mass (Da):70,524
Last modified:December 21, 2004 - v1
Checksum:i1276B82F82DAC561
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti93T → N in AAF89615 (Ref. 1) Curated1
Sequence conflicti475 – 476GI → AV in AAF89615 (Ref. 1) Curated2

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF167433 Genomic DNA. Translation: AAF89615.1.
AP008226 Genomic DNA. Translation: BAD71409.1.
RefSeqiWP_011228788.1. NC_006461.1.
YP_144852.1. NC_006461.1.

Genome annotation databases

EnsemblBacteriaiBAD71409; BAD71409; BAD71409.
GeneIDi3170041.
KEGGittj:TTHA1586.
PATRICi23958127. VBITheThe93045_1556.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF167433 Genomic DNA. Translation: AAF89615.1.
AP008226 Genomic DNA. Translation: BAD71409.1.
RefSeqiWP_011228788.1. NC_006461.1.
YP_144852.1. NC_006461.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1KIJX-ray2.30A/B1-390[»]
ProteinModelPortaliQ5SHZ4.
SMRiQ5SHZ4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi300852.TTHA1586.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD71409; BAD71409; BAD71409.
GeneIDi3170041.
KEGGittj:TTHA1586.
PATRICi23958127. VBITheThe93045_1556.

Phylogenomic databases

eggNOGiENOG4105C7D. Bacteria.
COG0187. LUCA.
HOGENOMiHOG000075156.
KOiK02470.
OMAiIKNMITA.
PhylomeDBiQ5SHZ4.

Miscellaneous databases

EvolutionaryTraceiQ9LCX5.

Family and domain databases

Gene3Di3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 1 hit.
HAMAPiMF_01898. GyrB. 1 hit.
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. 1 hit.
TIGRFAMsiTIGR01059. gyrB. 1 hit.
PROSITEiPS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiGYRB_THET8
AccessioniPrimary (citable) accession number: Q5SHZ4
Secondary accession number(s): Q9LCX5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 17, 2016
Last sequence update: December 21, 2004
Last modified: November 2, 2016
This is version 103 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

For the electron microscopy studies a GyrB-GyrA fusion protein was made with a Gly-Asp-Leu linker between the 2 subunits. It forms the expected dimer (PubMed:23804759).1 Publication
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

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.