DNA gyrase subunit B - Desulfotomaculum carboxydivorans (strain DSM 14880 / VKM B-2319 / CO-1-SRB)

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F6B3U6 (F6B3U6_DESCC) Unreviewed, UniProtKB/TrEMBL

Last modified May 1, 2013. Version 15. 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 HAMAP-Rule MF_01898 RuleBase RU003363
EC=5.99.1.3 HAMAP-Rule MF_01898 RuleBase RU003363

Gene names

Name:	gyrB HAMAP-Rule MF_01898
Ordered Locus Names:	Desca_0006

Organism

Desulfotomaculum carboxydivorans (strain DSM 14880 / VKM B-2319 / CO-1-SRB) [Complete proteome] [HAMAP] EMBL AEF92911.1

Taxonomic identifier

868595 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Clostridia › Clostridiales › Peptococcaceae › Desulfotomaculum ›

Protein attributes

Sequence length	636 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. HAMAP-Rule MF_01898 RuleBase RU003363
Catalytic activity	ATP-dependent breakage, passage and rejoining of double-stranded DNA. HAMAP-Rule MF_01898 RuleBase RU003363 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. HAMAP-Rule MF_01898 RuleBase RU000380 Contains 1 Toprim domain. HAMAP-Rule MF_01898

Ontologies

Keywords
Cellular component	Cytoplasm HAMAP-Rule MF_01898
Ligand	ATP-binding HAMAP-Rule MF_01898 RuleBase RU000380 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 HAMAP-Rule MF_01898 RuleBase RU000380 SAAS SAAS011557
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

421 – 535

115

Toprim By similarity HAMAP-Rule MF_01898

Sites

Metal binding

427

Magnesium 1; catalytic By similarity HAMAP-Rule MF_01898

Metal binding

500

Magnesium 1; catalytic By similarity HAMAP-Rule MF_01898

Metal binding

500

Magnesium 2 By similarity HAMAP-Rule MF_01898

Metal binding

502

Magnesium 2 By similarity HAMAP-Rule MF_01898

Site

452

Interaction with DNA By similarity HAMAP-Rule MF_01898

Site

455

Interaction with DNA By similarity HAMAP-Rule MF_01898

Sequences

Sequence

Length

Mass (Da)

Tools

F6B3U6 [UniParc].

Last modified July 27, 2011. Version 1.
Checksum: DCFB729937DCE535
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FASTA

636

71,081

        10         20         30         40         50         60 
MDQQINKYSA DQIQVLEGLE AVRRRPGMYI GSTSSRGLHH LVYEVVDNSI DEALAGFCNR 

        70         80         90        100        110        120 
ISVVIHKDNS VTVEDNGRGI PVDLHPKVGK PAVEVVLTML HAGGKFGGGG YKVSGGLHGV 

       130        140        150        160        170        180 
GVSVVNALSE KLEVEIKRNG NIYHQAYSRG VPVSELKIIG KSKSTGTKVT FKPDPEIFEE 

       190        200        210        220        230        240 
TTFSLETLAQ RLRELAYLNK GVKITIKDER KDPPVEQTFQ FDGGIRDFVK HLNRNKQVLH 

       250        260        270        280        290        300 
SKPIYVTGEK EQIIVEIALQ YNDTYNENIL SFANNIHTVD GGTHEIGFKT ALTRVVNDYG 

       310        320        330        340        350        360 
RNHNLLKNND PNLSGEDIRE GATVVISVKV REPQFEGQTK TKLGNSEVRG IVDSIFADGL 

       370        380        390        400        410        420 
ATYLEENPTV GKRIIEKAIT AARAREAARK ARELTRRKSA LDTMSLPGKL ADCSEKDPSV 

       430        440        450        460        470        480 
SELYLVEGDS AGGSAKQGRD RRFQAILPLR GKILNVEKAR MDKILANEEI RAMITALGCG 

       490        500        510        520        530        540 
IGQDFDISKA RYHKIIIMTD ADVDGAHIRT LLLTFFYRHM RPLIEAGYVY IAQPPLFRVR 

       550        560        570        580        590        600 
KGKLDSYVYS DHELEELLKR VGYDNVNIQR YKGLGEMNPE QLWETTMDPD TRTVLQVTLE 

       610        620        630 
DAIEADATFS MLMGDRVEPR RDFIQENAQY VRNLDI

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References

[1]

"Complete sequence of Desulfotomaculum carboxydivorans CO-1-SRB."
Lucas S., Han J., Lapidus A., Cheng J.-F., Goodwin L., Pitluck S., Peters L., Mikhailova N., Lu M., Han C., Tapia R., Land M., Hauser L., Kyrpides N., Ivanova N., Pagani I., Stams A., Plugge C.

Woyke T.
Submitted (MAY-2011) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: DSM 14880 / VKM B-2319 / CO-1-SRB.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP002736 Genomic DNA. Translation: AEF92911.1.
RefSeq	YP_004495823.1. NC_015565.1.
3D structure databases
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AEF92911; AEF92911; Desca_0006.
GeneID	10629349.
KEGG	dca:Desca_0006.
Organism-specific databases
CMR	Search...
Phylogenomic databases
KO	K02470.
Enzyme and pathway databases
BioCyc	DCAR868595:GHXC-6-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

F6B3U6_DESCC

Accession

Primary (citable) accession number: F6B3U6

Entry history

Integrated into UniProtKB/TrEMBL:	July 27, 2011
Last sequence update:	July 27, 2011
Last modified:	May 1, 2013
This is version 15 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

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information