DNA gyrase subunit B - Dictyoglomus thermophilum (strain ATCC 35947 / DSM 3960 / H-6-12)

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B5YFE9 (B5YFE9_DICT6) Unreviewed, UniProtKB/TrEMBL

Last modified May 29, 2013. Version 39. History...

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

Third-party data

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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 RuleBase RU003363 HAMAP-Rule MF_01898
EC=5.99.1.3 RuleBase RU003363 HAMAP-Rule MF_01898

Gene names

Name:	gyrB HAMAP-Rule MF_01898
Ordered Locus Names:	DICTH_1438

Organism

Dictyoglomus thermophilum (strain ATCC 35947 / DSM 3960 / H-6-12) [Complete proteome] [HAMAP] EMBL ACI19149.1

Taxonomic identifier

309799 [NCBI]

Taxonomic lineage

Bacteria › Dictyoglomi › Dictyoglomales › Dictyoglomaceae › Dictyoglomus ›

Protein attributes

Sequence length	635 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

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 SAAS011557
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. HAMAP-Rule MF_01898 RuleBase RU000380 Contains 1 Toprim domain. HAMAP-Rule MF_01898 SAAS SAAS011557

Ontologies

Keywords
Cellular component	Cytoplasm HAMAP-Rule MF_01898
Ligand	ATP-binding SAAS SAAS011557 HAMAP-Rule MF_01898 RuleBase RU000380 DNA-binding HAMAP-Rule MF_01898 Magnesium HAMAP-Rule MF_01898 Metal-binding HAMAP-Rule MF_01898 Nucleotide-binding
Molecular function	Isomerase Topoisomerase SAAS SAAS011557 HAMAP-Rule MF_01898 RuleBase RU000380
Technical term	Complete 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

418 – 533

116

Toprim By similarity HAMAP-Rule MF_01898

Sites

Metal binding

424

Magnesium 1; catalytic By similarity HAMAP-Rule MF_01898

Metal binding

498

Magnesium 1; catalytic By similarity HAMAP-Rule MF_01898

Metal binding

498

Magnesium 2 By similarity HAMAP-Rule MF_01898

Metal binding

500

Magnesium 2 By similarity HAMAP-Rule MF_01898

Site

449

Interaction with DNA By similarity HAMAP-Rule MF_01898

Site

452

Interaction with DNA By similarity HAMAP-Rule MF_01898

Sequences

Sequence

Length

Mass (Da)

Tools

B5YFE9 [UniParc].

Last modified November 25, 2008. Version 1.
Checksum: F604B971605140A1
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FASTA

635

72,129

        10         20         30         40         50         60 
MAVTKKDKYT ADSIQILEGT EAVRRRPGMY IGDTGVRGLH HLIFELVDNS IDEVMAGYCD 

        70         80         90        100        110        120 
YILVELKKDG AVVVADNGRG IPVDIHPQAK KPALEVVLTT LHAGGKFSNS IYKISGGLHG 

       130        140        150        160        170        180 
VGLSVVNALS SKLEVEVMRD GKIFYQVYER GKPITPLTVK GETDKTGTKI KFYPDPEIFE 

       190        200        210        220        230        240 
TTKFDYDIVA NRLRELAFLN PKVTIELRDE RTGRSNIFKY EGGLLEFIEY LSKGKEVLHE 

       250        260        270        280        290        300 
PIYMEREEGN LILEIVMQYN SGYDELILSY VNNIHTIEGG THVTGFRTAL TRVVNNFARS 

       310        320        330        340        350        360 
WGLWKENESL SGDDVREGLT AIVSVKVPDP QFEGQTKTKL GNTEVRKFVE KVVEEELTEY 

       370        380        390        400        410        420 
FSKNPDTGKL IITKIIEAYR ARQAARKARE LVRRKSLLES TLLPGKLADC SEKDPAKCEL 

       430        440        450        460        470        480 
FIVEGESAGG SAKQARDRRY QAILPLRGKI LNVEKAQHLT KILSSEEIKA IIASLGTGIG 

       490        500        510        520        530        540 
QDFDLSKLRY HKIIIMTDAD VDGAHIRTLL LTFFYRHFRP LIEGGYIYIA QPPLYLLRKG 

       550        560        570        580        590        600 
KEERYAYSEE EKEEILKEWG YPENVYIQRY KGLGEMDPEQ LRETTMDPQK RILLQVTIED 

       610        620        630 
ALEAERLFSI LMGNNVEERR NFIEQKAKFV RNLDI

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References

[1]

"The complete genome sequence of Dictyoglomus thermophilum strain ATCC 35947 / DSM 3960 / H-6-12."
Dodson R.J., Durkin A.S., Wu M., Eisen J., Sutton G.
Submitted (AUG-2008) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 35947 / DSM 3960 / H-6-12.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP001146 Genomic DNA. Translation: ACI19149.1.
RefSeq	YP_002251257.1. NC_011297.1.
3D structure databases
ProteinModelPortal	B5YFE9.
ModBase	Search...
Protein-protein interaction databases
STRING	309799.DICTH_1438.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	ACI19149; ACI19149; DICTH_1438.
GeneID	6945060.
KEGG	dth:DICTH_1438.
PATRIC	21807500. VBIDicThe33784_1381.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0187.
HOGENOM	HOG000075156.
KO	K02470.
OMA	IFETTEF.
ProtClustDB	PRK05644.
Enzyme and pathway databases
BioCyc	DTHE309799:GHF9-1425-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. 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.
ProtoNet	Search...

Entry information

Entry name

B5YFE9_DICT6

Accession

Primary (citable) accession number: B5YFE9

Entry history

Integrated into UniProtKB/TrEMBL:	November 25, 2008
Last sequence update:	November 25, 2008
Last modified:	May 29, 2013
This is version 39 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

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information