DNA gyrase subunit B - Pseudomonas stutzeri (strain A1501)

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A4VFG1 (A4VFG1_PSEU5) Unreviewed, UniProtKB/TrEMBL

Last modified May 1, 2013. Version 45. 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 EMBL ABP77712.1
Ordered Locus Names:	PST_0004 EMBL ABP77712.1

Organism

Pseudomonas stutzeri (strain A1501) [Complete proteome] [HAMAP] EMBL ABP77712.1

Taxonomic identifier

379731 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Pseudomonadales › Pseudomonadaceae › Pseudomonas ›

Protein attributes

Sequence length	804 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 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

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

A4VFG1 [UniParc].

Last modified May 29, 2007. Version 1.
Checksum: 1154BAE30C4AAC4A
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FASTA

804

90,024

        10         20         30         40         50         60 
MSENHTYDSS SIKVLKGLDA VRKRPGMYIG DTDDGTGLHH MVFEVVDNSI DEALAGYCSD 

        70         80         90        100        110        120 
ISITIHTDES ITVRDNGRGI PVDIHEEGVS AAEVIMTVLH AGGKFDDNSY KVSGGLHGVG 

       130        140        150        160        170        180 
VSVVNALSEE LLLTIRREGK VWEQLYRHGV PQAPLAAVGE TDTSGTQIHF KPSAETFQNI 

       190        200        210        220        230        240 
HFSWDILAKR LRELSFLNSG VGIVLRDERT AKEELFKYEG GLSAFVAYLN TNKTAVNQVF 

       250        260        270        280        290        300 
HFNVQRDDGV GVEVALQWND SFNENILCFT NNIPQRDGGT HLAGFRSALT RNLNNYIEQE 

       310        320        330        340        350        360 
GLAKKHKIAT TGDDAREGLT AIISVKVPDP KFSSQTKDKL VSSEVKTAVE QEMGKYFADF 

       370        380        390        400        410        420 
LLEHPNEAKA VVGKMIDAAR AREAARKARE MTRRKGALDI AGLPGKLADC QEKDPALSEL 

       430        440        450        460        470        480 
YIVEGDSAGG SAKQGRNRKT QAILPLKGKI LNVEKARFDK MLSSQEVGTL ITALGCGIGR 

       490        500        510        520        530        540 
EEYNIDKLRY HNIIIMTDAD VDGSHIRTLL LTFFFRQLPE LIERGYVYIA QPPLYKVKRG 

       550        560        570        580        590        600 
KQEQYIKDDE AMEEYLTQSA LEEASLHVNE DAPGLAGEAL ERLVNDYRTV MKTLQRLSRL 

       610        620        630        640        650        660 
YPLELTEHFI YLPRVTLEQL ADHSAMQAWL EQYSARLKAG ERSGLIYNLS LREDKERHLW 

       670        680        690        700        710        720 
LPEVEISSHG LASYITFNRD FFGSNDYRTV TALGEKLNSL LEEGAYVQRG ERKKPVASFK 

       730        740        750        760        770        780 
EALDWLMNEG TRRHSVQRYK GLGEMNPDQL WETTMDPNVR RMLKVTIEDA IAADQIFNTL 

       790        800 
MGDAVEPRRE FIETNALAVS NLDF

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References

[1]

"Complete genome sequence of the metabolically versatile and root-associated nitrogen-fixing bacterium Pseudomonas stutzeri A1501."
Yan Y., Yang J., Dou Y., Ping S., Chen M., Yao Z., Li H., Lu W., Zhang W., Peng J., Liu W., He S., Geng L., Zhang X., Yang F., Li D., Lin Z., Wang Y.

Jin Q.
Submitted (APR-2006) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: A1501.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000304 Genomic DNA. Translation: ABP77712.1.
RefSeq	YP_001170554.1. NC_009434.1.
3D structure databases
ProteinModelPortal	A4VFG1.
ModBase	Search...
Protein-protein interaction databases
STRING	379731.PST_0004.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	ABP77712; ABP77712; PST_0004.
GeneID	5095079.
KEGG	psa:PST_0004.
PATRIC	19960413. VBIPseStu31643_0004.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0187.
HOGENOM	HOG000075155.
KO	K02470.
OMA	IFETTEF.
ProtClustDB	PRK14939.
Enzyme and pathway databases
BioCyc	PSTU379731:GJER-4-MONOMER.
Family and domain databases
Gene3D	3.30.230.10. 1 hit. 3.30.565.10. 1 hit. 3.40.50.670. 2 hits.
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

A4VFG1_PSEU5

Accession

Primary (citable) accession number: A4VFG1

Entry history

Integrated into UniProtKB/TrEMBL:	May 29, 2007
Last sequence update:	May 29, 2007
Last modified:	May 1, 2013
This is version 45 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