DNA gyrase subunit B - Salmonella paratyphi A (strain ATCC 9150 / SARB42)

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Q5PKU9 (Q5PKU9_SALPA) Unreviewed, UniProtKB/TrEMBL

Last modified May 1, 2013. Version 69. 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 AAV79471.1
Ordered Locus Names:	SPA3679

Organism

Salmonella paratyphi A (strain ATCC 9150 / SARB42) [Complete proteome] [HAMAP]

Taxonomic identifier

295319 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Salmonella ›

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. SAAS SAAS013506 RuleBase RU003363 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 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

Q5PKU9 [UniParc].

Last modified January 4, 2005. Version 1.
Checksum: B882B35FA10451B1
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FASTA

804

89,910

        10         20         30         40         50         60 
MSNSYDSSSI KVLKGLDAVR KRPGMYIGDT DDGTGLHHMV FEVVDNAIDE ALAGHCKDIV 

        70         80         90        100        110        120 
VTIHADNSVS VTDDGRGIPT GIHPEEGVSA AEVIMTVLHA GGKFDDNSYK VSGGLHGVGV 

       130        140        150        160        170        180 
SVVNALSQKL ELVIQRDGKI HRQIYEHGVP QAPLAVTGDT DKTGTMVRFW PSHETFTNVT 

       190        200        210        220        230        240 
EFEYEILAKR LRELSFLNSG VSIRLRDKRD GKEDHFHYEG GIKAFVEYLN KNKTPIHPNI 

       250        260        270        280        290        300 
FYFSTEKDGI GIEVALQWND GFQENIYCFT NNIPQRDGGT HLAGFRAAMT RTLNAYMDKE 

       310        320        330        340        350        360 
GYSKKAKVSA TGDDAREGLI AVVSVKVPDP KFSSQTKDKL VSSEVKSAVE QQMNELLSEY 

       370        380        390        400        410        420 
LLENPSDAKI VVGKIIDAAR AREAARRARE MTRRKGALDL AGLPGKLADC QERDPALSEL 

       430        440        450        460        470        480 
YLVEGDSAGG SAKQGRNRKN QAILPLKGKI LNVEKARFDK MLSSQEVATL ITALGCGIGR 

       490        500        510        520        530        540 
DEYNPDKLRY HSIIIMTDAD VDGSHIRTLL LTFFYRQMPE IVERGHVYIA QPPLYKVKKG 

       550        560        570        580        590        600 
KQEQYIKDDE AMDQYQISIA LDGATLHANA HAPALSGEAL EKLVSEYNAT QKMIGRMERR 

       610        620        630        640        650        660 
FPKALLKELV YQPTLTEADL SDEQTVTRWV NALITELNEK EQHGSQWKFD VHTNTEQNLF 

       670        680        690        700        710        720 
EPIVRVRTHG VDTDYPLDHE FVTGAEYRRI CTLGEKLRGL IEEDAFIERG ERRQPVTSFE 

       730        740        750        760        770        780 
QALEWLVKES RRGLAIQRYK GLGEMNPDQL WETTMDPESR RMLRVTVKDA IAADQLFTTL 

       790        800 
MGDAVEPRRA FIEENALKAA NIDI

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References

[1]

"Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid."
McClelland M., Sanderson K.E., Clifton S.W., Latreille P., Porwollik S., Sabo A., Meyer R., Bieri T., Ozersky P., McLellan M., Harkins C.R., Wang C., Nguyen C., Berghoff A., Elliott G., Kohlberg S., Strong C., Du F.

Wilson R.K.
Nat. Genet. 36:1268-1274(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 9150 / SARB42.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000026 Genomic DNA. Translation: AAV79471.1.
RefSeq	YP_152783.1. NC_006511.1.
3D structure databases
ProteinModelPortal	Q5PKU9.
SMR	Q5PKU9. Positions 10-392.
ModBase	Search...
Protein-protein interaction databases
STRING	295319.SPA3679.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAV79471; AAV79471; SPA3679.
GeneID	3175978.
KEGG	spt:SPA3679.
PATRIC	32357086. VBISalEnt134188_3924.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	HOG000075155.
KO	K02470.
OMA	IFETTEF.
ProtClustDB	PRK14939.
Enzyme and pathway databases
BioCyc	SENT295319:GJBZ-3677-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

Q5PKU9_SALPA

Accession

Primary (citable) accession number: Q5PKU9

Entry history

Integrated into UniProtKB/TrEMBL:	January 4, 2005
Last sequence update:	January 4, 2005
Last modified:	May 1, 2013
This is version 69 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