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Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Enterococcus faecalis (strain ATCC 700802 / V583)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

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.UniRule annotation2 Publications

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

Enzyme regulationi

Pyrrolopyrimidines inhibit both GyrB and its paralog in topoisomerase IV (parE) (PubMed:23352267).2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi428 – 4281Magnesium 1; catalyticUniRule annotation
Metal bindingi501 – 5011Magnesium 1; catalyticUniRule annotation
Metal bindingi501 – 5011Magnesium 2UniRule annotation
Metal bindingi503 – 5031Magnesium 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

Enzyme and pathway databases

BioCyciEFAE226185:GHI1-5-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:EF_0005
OrganismiEnterococcus faecalis (strain ATCC 700802 / V583)
Taxonomic identifieri226185 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesEnterococcaceaeEnterococcus
Proteomesi
  • UP000001415 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 – 642642DNA gyrase subunit BPRO_0000435540Add
BLAST

Interactioni

Subunit structurei

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.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei453 – 4531Interaction with DNAUniRule annotation
Sitei456 – 4561Interaction with DNAUniRule annotation

Protein-protein interaction databases

STRINGi226185.EF0005.

Structurei

Secondary structure

1
642
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi19 – 246Combined sources
Helixi26 – 305Combined sources
Helixi35 – 5420Combined sources
Beta strandi60 – 656Combined sources
Beta strandi71 – 755Combined sources
Turni86 – 883Combined sources
Beta strandi89 – 913Combined sources
Helixi92 – 987Combined sources
Helixi122 – 1276Combined sources
Beta strandi129 – 13810Combined sources
Beta strandi141 – 1488Combined sources
Beta strandi157 – 1615Combined sources
Beta strandi166 – 1738Combined sources
Turni175 – 1773Combined sources
Helixi186 – 19914Combined sources
Turni200 – 2023Combined sources
Beta strandi204 – 2096Combined sources
Beta strandi216 – 2216Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4GEEX-ray1.70A18-224[»]
4GFNX-ray1.90A18-224[»]
4GGLX-ray1.69A18-224[»]
4HXWX-ray1.69A18-224[»]
4K4OX-ray1.30A18-224[»]
4KSGX-ray1.75A18-224[»]
4KSHX-ray1.70A18-224[»]
4KTNX-ray1.69A18-224[»]
ProteinModelPortaliQ839Z1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini422 – 536115ToprimUniRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

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

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.
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.

Q839Z1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRERAQEYDA SQIQVLEGLE AVRKRPGMYI GSTSGEGLHH LVWEIVDNSI
60 70 80 90 100
DEALAGFAKS IQVIIEPDDS ITVIDDGRGI PVGIQAKTGR PAVETVFTVL
110 120 130 140 150
HAGGKFGGGG YKVSGGLHGV GSSVVNALST SLDVRVYKDG KVYYQEYRRG
160 170 180 190 200
AVVDDLKVIE ETDRHGTTVH FIPDPEIFTE TTVYDFDKLA TRVRELAFLN
210 220 230 240 250
RGLHISIEDR REGQEDKKEY HYEGGIKSYV EHLNANKDVI FPEPIFIEGE
260 270 280 290 300
QQDITVEVSM QYTDGYHSNI LSFANNIHTY EGGTHESGFK TSLTRVINDY
310 320 330 340 350
ARKQKLMKEN DEKLTGEDVR EGLTAVVSIK HPDPQFEGQT KTKLGNSEVR
360 370 380 390 400
TVTDRLFSEY FTKFLMENPT VGKQIVEKGM LASKARLAAK RAREVTRRKG
410 420 430 440 450
ALEISNLPGK LADCSSKDPE KCELFIVEGD SAGGSAKQGR SREFQAILPI
460 470 480 490 500
RGKILNVEKA SMDKILANEE IRSLFTAMGT GFGEDFDVSK ARYHKLVIMT
510 520 530 540 550
DADVDGAHIR TLLLTLFYRF MRPIVEAGYV YIAQPPLYGV KQGKNITYVQ
560 570 580 590 600
PGKHAEEELA KVLEELPASP KPSVQRYKGL GEMDDHQLWE TTMDPEKRLM
610 620 630 640
ARVSVDDAIE ADQIFEMLMG DRVEPRRAFI EENAHYVKNL DI
Length:642
Mass (Da):71,878
Last modified:June 1, 2003 - v1
Checksum:i7A5FD53203C6AEE0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016830 Genomic DNA. Translation: AAO79890.1.
RefSeqiNP_813818.1. NC_004668.1.
WP_002379278.1. NC_004668.1.

Genome annotation databases

EnsemblBacteriaiAAO79890; AAO79890; EF_0005.
GeneIDi1198916.
KEGGiefa:EF0005.
PATRICi21850447. VBIEntFae7065_0005.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016830 Genomic DNA. Translation: AAO79890.1.
RefSeqiNP_813818.1. NC_004668.1.
WP_002379278.1. NC_004668.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4GEEX-ray1.70A18-224[»]
4GFNX-ray1.90A18-224[»]
4GGLX-ray1.69A18-224[»]
4HXWX-ray1.69A18-224[»]
4K4OX-ray1.30A18-224[»]
4KSGX-ray1.75A18-224[»]
4KSHX-ray1.70A18-224[»]
4KTNX-ray1.69A18-224[»]
ProteinModelPortaliQ839Z1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi226185.EF0005.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAO79890; AAO79890; EF_0005.
GeneIDi1198916.
KEGGiefa:EF0005.
PATRICi21850447. VBIEntFae7065_0005.

Phylogenomic databases

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

Enzyme and pathway databases

BioCyciEFAE226185:GHI1-5-MONOMER.

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.
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...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700802 / V583.
  2. "Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV (ParE). Part I: Structure guided discovery and optimization of dual targeting agents with potent, broad-spectrum enzymatic activity."
    Tari L.W., Trzoss M., Bensen D.C., Li X., Chen Z., Lam T., Zhang J., Creighton C.J., Cunningham M.L., Kwan B., Stidham M., Shaw K.J., Lightstone F.C., Wong S.E., Nguyen T.B., Nix J., Finn J.
    Bioorg. Med. Chem. Lett. 23:1529-1536(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.69 ANGSTROMS) OF 18-224 IN COMPLEX WITH INHIBITORS, FUNCTION, ENZYME REGULATION.
  3. Cited for: X-RAY CRYSTALLOGRAPHY (1.30 ANGSTROMS) OF 18-224 IN COMPLEX WITH INHIBITORS, FUNCTION, ENZYME REGULATION.

Entry informationi

Entry nameiGYRB_ENTFA
AccessioniPrimary (citable) accession number: Q839Z1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 17, 2016
Last sequence update: June 1, 2003
Last modified: April 13, 2016
This is version 112 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.