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Q839Z1

- Q839Z1_ENTFA

UniProt

Q839Z1 - Q839Z1_ENTFA

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Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Enterococcus faecalis (strain ATCC 700802 / V583)
Status
Unreviewed - Annotation score: 3 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 annotation

Catalytic activityi

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

Cofactori

Note: Magnesium. Binds two Mg(2+) per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn(2+) and Ca(2+).UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi428 – 4281Magnesium 1; catalyticUniRule annotation
Sitei453 – 4531Interaction with DNAUniRule annotation
Sitei456 – 4561Interaction with DNAUniRule annotation
Metal bindingi501 – 5011Magnesium 1; catalyticUniRule annotation
Metal bindingi501 – 5011Magnesium 2UniRule annotation
Metal bindingi503 – 5031Magnesium 2UniRule annotation

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-HAMAP
  2. DNA binding Source: UniProtKB-HAMAP
  3. DNA topoisomerase type II (ATP-hydrolyzing) activity Source: UniProtKB-HAMAP
  4. magnesium ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. DNA-dependent DNA replication Source: UniProtKB-HAMAP
  2. DNA topological change Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Isomerase, TopoisomeraseUniRule annotation

Keywords - Ligandi

ATP-bindingUniRule annotation, DNA-bindingUniRule annotation, MagnesiumUniRule annotation, Metal-bindingUniRule annotation, 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 annotationImported
Ordered Locus Names:EF_0005Imported
OrganismiEnterococcus faecalis (strain ATCC 700802 / V583)Imported
Taxonomic identifieri226185 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesEnterococcaceaeEnterococcus
ProteomesiUP000001415: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

  1. chromosome Source: InterPro
  2. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

CytoplasmUniRule annotation

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

Protein-protein interaction databases

STRINGi226185.EF0005.

Structurei

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
Contains Toprim domain.SAAS annotation

Phylogenomic databases

KOiK02470.
OMAiEYHRGAP.
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.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR013760. Topo_IIA_like_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.

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 .
RefSeqi NP_813818.1. NC_004668.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
4GEE X-ray 1.70 A 18-224 [» ]
4GFN X-ray 1.90 A 18-224 [» ]
4GGL X-ray 1.69 A 18-224 [» ]
4HXW X-ray 1.69 A 18-224 [» ]
4K4O X-ray 1.30 A 18-224 [» ]
4KSG X-ray 1.75 A 18-224 [» ]
4KSH X-ray 1.70 A 18-224 [» ]
4KTN X-ray 1.69 A 18-224 [» ]
ProteinModelPortali Q839Z1.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 226185.EF0005.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAO79890 ; AAO79890 ; EF_0005 .
GeneIDi 1198916.
KEGGi efa:EF0005.
PATRICi 21850447. VBIEntFae7065_0005.

Phylogenomic databases

KOi K02470.
OMAi EYHRGAP.
OrthoDBi EOG6P334W.

Enzyme and pathway databases

BioCyci EFAE226185:GHI1-5-MONOMER.

Family and domain databases

Gene3Di 3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 1 hit.
HAMAPi MF_01898. GyrB.
InterProi 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.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR013760. Topo_IIA_like_dom.
IPR018522. TopoIIA_CS.
IPR006171. Toprim_domain.
[Graphical view ]
Pfami PF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view ]
PRINTSi PR00418. TPI2FAMILY.
SMARTi SM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view ]
SUPFAMi SSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 1 hit.
TIGRFAMsi TIGR01059. gyrB. 1 hit.
PROSITEi PS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700802 / V583Imported.
  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.
  3. "A new class of type IIA topoisomerase inhibitors with broad-spectrum antibacterial activity."
    Tari L.W., Bensen D.C., Finn J.
    Submitted (APR-2013) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.30 ANGSTROMS) OF 18-224.
  4. "A new class of type iia topoisomerase inhibitors with broad-spectrum antibacterial activity."
    Tari L.W., Bensen D.C., Finn J.
    Submitted (MAY-2013) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 18-224.
  5. "A new class of type iia topoisomerase inhibitors withbroad-spectrum antibacterial activity."
    Tari L.W., Bensen D.C., Finn J.
    Submitted (MAY-2013) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) OF 18-224.

Entry informationi

Entry nameiQ839Z1_ENTFA
AccessioniPrimary (citable) accession number: Q839Z1
Entry historyi
Integrated into UniProtKB/TrEMBL: June 1, 2003
Last sequence update: June 1, 2003
Last modified: November 26, 2014
This is version 100 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureImported, Complete proteome, Reference proteomeImported

External Data

Dasty 3