DNA gyrase subunit B - Enterococcus faecalis (strain ATCC 700802 / V583)

Contribute

Send feedback

Read comments (?) or add your own

Q839Z1 (Q839Z1_ENTFA) Unreviewed, UniProtKB/TrEMBL

Last modified May 1, 2013. Version 84. History...

Clusters with 100%, 90%, 50% identity |

Third-party data

text xml rdf/xml gff fasta

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info Customize order

Names and origin

Protein names

Recommended name:
DNA gyrase subunit B HAMAP-Rule MF_01898
EC=5.99.1.3 HAMAP-Rule MF_01898

Gene names

Name:	gyrB HAMAP-Rule MF_01898 EMBL AAO79890.1
Ordered Locus Names:	EF_0005 EMBL AAO79890.1

Organism

Enterococcus faecalis (strain ATCC 700802 / V583) [Reference proteome] [HAMAP] EMBL AAO79890.1

Taxonomic identifier

226185 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacilli › Lactobacillales › Enterococcaceae › Enterococcus ›

Protein attributes

Sequence length	642 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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 By similarity. RuleBase RU003363 HAMAP-Rule MF_01898
Catalytic activity	ATP-dependent breakage, passage and rejoining of double-stranded DNA. RuleBase RU003363 HAMAP-Rule MF_01898 SAAS SAAS013506
Cofactor	Magnesium. 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⁺ and Ca²⁺ By similarity. HAMAP-Rule MF_01898
Subunit structure	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 By similarity. HAMAP-Rule MF_01898
Subcellular location	Cytoplasm By similarity HAMAP-Rule MF_01898.
Sequence similarities	Belongs to the type II topoisomerase family. RuleBase RU000380 HAMAP-Rule MF_01898 Contains 1 Toprim domain. HAMAP-Rule MF_01898

Ontologies

Keywords
Cellular component	Cytoplasm HAMAP-Rule MF_01898
Ligand	ATP-binding RuleBase RU000380 HAMAP-Rule MF_01898 SAAS SAAS011557 DNA-binding HAMAP-Rule MF_01898 Magnesium HAMAP-Rule MF_01898 Metal-binding HAMAP-Rule MF_01898 Nucleotide-binding
Molecular function	Isomerase Topoisomerase RuleBase RU000380 HAMAP-Rule MF_01898 SAAS SAAS011557
Technical term	3D-structure PDB 4GEE PDB 4GFN PDB 4GGL PDB 4HXW Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA topological change Inferred from electronic annotation. Source: InterPro DNA-dependent DNA replication Inferred from electronic annotation. Source: HAMAP
Cellular_component	chromosome Inferred from electronic annotation. Source: InterPro cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: HAMAP DNA topoisomerase type II (ATP-hydrolyzing) activity Inferred from electronic annotation. Source: HAMAP metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Regions

Domain

422 – 536

115

Toprim By similarity HAMAP-Rule MF_01898

Sites

Metal binding

428

Magnesium 1; catalytic By similarity HAMAP-Rule MF_01898

Metal binding

501

Magnesium 1; catalytic By similarity HAMAP-Rule MF_01898

Metal binding

501

Magnesium 2 By similarity HAMAP-Rule MF_01898

Metal binding

503

Magnesium 2 By similarity HAMAP-Rule MF_01898

Site

453

Interaction with DNA By similarity HAMAP-Rule MF_01898

Site

456

Interaction with DNA By similarity HAMAP-Rule MF_01898

Sequences

Sequence

Length

Mass (Da)

Tools

Q839Z1 [UniParc].

Last modified June 1, 2003. Version 1.
Checksum: 7A5FD53203C6AEE0
Show »

FASTA

642

71,878

        10         20         30         40         50         60 
MRERAQEYDA SQIQVLEGLE AVRKRPGMYI GSTSGEGLHH LVWEIVDNSI DEALAGFAKS 

        70         80         90        100        110        120 
IQVIIEPDDS ITVIDDGRGI PVGIQAKTGR PAVETVFTVL HAGGKFGGGG YKVSGGLHGV 

       130        140        150        160        170        180 
GSSVVNALST SLDVRVYKDG KVYYQEYRRG AVVDDLKVIE ETDRHGTTVH FIPDPEIFTE 

       190        200        210        220        230        240 
TTVYDFDKLA TRVRELAFLN RGLHISIEDR REGQEDKKEY HYEGGIKSYV EHLNANKDVI 

       250        260        270        280        290        300 
FPEPIFIEGE QQDITVEVSM QYTDGYHSNI LSFANNIHTY EGGTHESGFK TSLTRVINDY 

       310        320        330        340        350        360 
ARKQKLMKEN DEKLTGEDVR EGLTAVVSIK HPDPQFEGQT KTKLGNSEVR TVTDRLFSEY 

       370        380        390        400        410        420 
FTKFLMENPT VGKQIVEKGM LASKARLAAK RAREVTRRKG ALEISNLPGK LADCSSKDPE 

       430        440        450        460        470        480 
KCELFIVEGD SAGGSAKQGR SREFQAILPI RGKILNVEKA SMDKILANEE IRSLFTAMGT 

       490        500        510        520        530        540 
GFGEDFDVSK ARYHKLVIMT DADVDGAHIR TLLLTLFYRF MRPIVEAGYV YIAQPPLYGV 

       550        560        570        580        590        600 
KQGKNITYVQ PGKHAEEELA KVLEELPASP KPSVQRYKGL GEMDDHQLWE TTMDPEKRLM 

       610        620        630        640 
ARVSVDDAIE ADQIFEMLMG DRVEPRRAFI EENAHYVKNL DI

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis." Paulsen I.T., Banerjei L., Myers G.S.A., Nelson K.E., Seshadri R., Read T.D., Fouts D.E., Eisen J.A., Gill S.R., Heidelberg J.F., Tettelin H., Dodson R.J., Umayam L.A., Brinkac L.M., Beanan M.J., Daugherty S.C., DeBoy R.T., Durkin S.A. Fraser C.M. Science 299:2071-2074(2003) [PubMed] [Europe PMC] [Abstract] 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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE016830 Genomic DNA. Translation: AAO79890.1.

RefSeq

NP_813818.1. NC_004668.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

HSSP

HSSP built from PDB template 1AJ6 based on UniProtKB P06982.

ProteinModelPortal

Q839Z1.

ModBase

Search...

Protein-protein interaction databases

STRING

226185.EF0005.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAO79890; AAO79890; EF_0005.

GeneID

1198916.

KEGG

efa:EF0005.

PATRIC

21850447. VBIEntFae7065_0005.

Phylogenomic databases

K02470.

OMA

IFETTEF.

ProtClustDB

PRK05644.

Enzyme and pathway databases

BioCyc

EFAE226185:GHI1-160-MONOMER.

Family and domain databases

Gene3D

3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 1 hit.

HAMAP

MF_01898. GyrB.

InterPro

IPR002288. DNA_gyrase_B_C.
IPR011557. GyrB.
IPR003594. HATPase_ATP-bd.
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]

Pfam

PF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]

PRINTS

PR00418. TPI2FAMILY.

SMART

SM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view]

SUPFAM

SSF55874. ATP_bd_ATPase. 1 hit.
SSF54211. Ribosomal_S5_D2-typ_fold. 1 hit.
SSF56719. Topo_IIA_cen. 1 hit.

TIGRFAMs

TIGR01059. gyrB. 1 hit.

PROSITE

PS00177. TOPOISOMERASE_II. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

Q839Z1_ENTFA

Accession

Primary (citable) accession number: Q839Z1

Entry history

Integrated into UniProtKB/TrEMBL:	June 1, 2003
Last sequence update:	June 1, 2003
Last modified:	May 1, 2013
This is version 84 of the entry and version 1 of the sequence. [Complete history]

Entry status

Unreviewed (UniProtKB/TrEMBL)

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Regions

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information