DNA gyrase subunit B - Paenibacillus sp. (strain JDR-2)

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C6CT02 (C6CT02_PAESJ) Unreviewed, UniProtKB/TrEMBL

Last modified May 1, 2013. Version 35. History...

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

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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:	Pjdr2_0006

Organism

Paenibacillus sp. (strain JDR-2) [Complete proteome] [HAMAP] EMBL ACS98686.1

Taxonomic identifier

324057 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacilli › Bacillales › Paenibacillaceae › Paenibacillus

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 SAAS SAAS013506 HAMAP-Rule MF_01898
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 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

419 – 533

115

Toprim By similarity HAMAP-Rule MF_01898

Sites

Metal binding

425

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

450

Interaction with DNA By similarity HAMAP-Rule MF_01898

Site

453

Interaction with DNA By similarity HAMAP-Rule MF_01898

Sequences

Sequence

Length

Mass (Da)

Tools

C6CT02 [UniParc].

Last modified September 1, 2009. Version 1.
Checksum: 54F26DD046F1B99C
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FASTA

635

70,974

        10         20         30         40         50         60 
MSQQNTYDES QIQVLEGLEA VRKRPGMYIG STSGKGLHHL VWEVVDNSID EALAGYCTKI 

        70         80         90        100        110        120 
QVRVHEDNSI TVIDNGRGIP VGENAKLKKS TLEVVMTVLH AGGKFGGEGY KVSGGLHGVG 

       130        140        150        160        170        180 
VSVVNALSEH VTVTVKLHGN VYQQEYRRGV PQYDVKIIGE SDETGTTVKF KPDPEIFTDT 

       190        200        210        220        230        240 
TVYEYETLQS RIRELAFLNK GLEIELIDER TGTSNSFKYD GGIIEFVKHL NRNKEVMHEE 

       250        260        270        280        290        300 
PIYVEGSKDH IQVEVSLQYN DGYTENIHSF ANNINTHEGG THESGFKSAL TRIINDYARK 

       310        320        330        340        350        360 
TGLIKDNDSN FSGDDVREGL TAIISVKIPE PQFEGQTKTK LGNSEVRGIV ESFFAEKLQE 

       370        380        390        400        410        420 
FLDENPSVSR KIVEKGLQAA RAREAARKAR ELTRRKSALE VSSLPGKLAD CSSKDASISE 

       430        440        450        460        470        480 
LYIVEGDSAG GSAKQGRDRH FQAILPLRGK ILNVERARLD RILGNAEIRA IITALGTGIG 

       490        500        510        520        530        540 
DDFDLAKARY HKVIIMTDAD VDGAHIRTLM LTFFFRYMRK IIEAGYIYIA QPPLFKIERN 

       550        560        570        580        590        600 
KVIRYAQSEK EREEIIAEFG EGAKVNVQRY KGLGEMNATQ LWETTMDPES RTMLQVSIED 

       610        620        630 
AIEADVIFDT LMGDNVEPRR DFIQQFAKDV KNLDI

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References

[1]

"Complete genome sequence of Paenibacillus sp. strain JDR-2."
Chow V., Nong G., St John F.J., Rice J.D., Dickstein E., Chertkov O., Bruce D., Detter C., Brettin T., Han J., Woyke T., Pitluck S., Nolan M., Pati A., Martin J., Copeland A., Land M.L., Goodwin L.

Preston J.F.
Stand. Genomic Sci. 6:1-10(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: JDR-2.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP001656 Genomic DNA. Translation: ACS98686.1.
RefSeq	YP_003008773.1. NC_012914.1.
3D structure databases
ProteinModelPortal	C6CT02.
SMR	C6CT02. Positions 14-217.
ModBase	Search...
Protein-protein interaction databases
STRING	324057.Pjdr2_0006.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	ACS98686; ACS98686; Pjdr2_0006.
GeneID	8126979.
KEGG	pjd:Pjdr2_0006.
PATRIC	22830403. VBIPaeSp118865_0006.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0187.
HOGENOM	HOG000075155.
KO	K02470.
OMA	IFETTEF.
ProtClustDB	PRK05644.
Enzyme and pathway databases
BioCyc	PSP324057:GH5H-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

C6CT02_PAESJ

Accession

Primary (citable) accession number: C6CT02

Entry history

Integrated into UniProtKB/TrEMBL:	September 1, 2009
Last sequence update:	September 1, 2009
Last modified:	May 1, 2013
This is version 35 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