DNA gyrase subunit B - Shigella flexneri

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P0AES8 (GYRB_SHIFL) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 62. History...

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

Documents (1) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
DNA gyrase subunit B
EC=5.99.1.3

Gene names

Name:	gyrB
Ordered Locus Names:	SF3765, S4006

Organism

Shigella flexneri [Complete proteome] [HAMAP]

Taxonomic identifier

623 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Shigella

Protein attributes

Sequence length	804 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
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
Catalytic activity	ATP-dependent breakage, passage and rejoining of double-stranded DNA. 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.
Enzyme regulation	Target of two classes of inhibitors, coumarins and quinolones. Coumarins bind to GyrB and are competitive inhibitors with respect to ATP. Quinolones bind DNA gyrase when the enzyme is complexed with DNA and trap the enzyme in an abortive ternary complex 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.
Subcellular location	Cytoplasm Potential HAMAP-Rule MF_01898.
Sequence similarities	Belongs to the type II topoisomerase family. Contains 1 Toprim domain.

Ontologies

Keywords
Biological process	Antibiotic resistance
Cellular component	Cytoplasm
Ligand	ATP-binding DNA-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Isomerase Topoisomerase
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 response to antibiotic Inferred from electronic annotation. Source: UniProtKB-KW
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

Molecule processing

Initiator methionine

Removed By similarity

Chain

2 – 804

803

DNA gyrase subunit B HAMAP-Rule MF_01898

PRO_0000145335

Regions

Domain

418 – 533

116

Toprim

Sites

Metal binding

424

Magnesium 1; catalytic By similarity

Metal binding

498

Magnesium 1; catalytic By similarity

Metal binding

498

Magnesium 2 By similarity

Metal binding

500

Magnesium 2 By similarity

Site

449

Interaction with DNA By similarity

Site

452

Interaction with DNA By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

P0AES8 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: D831B95FFB3A7EE3
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FASTA

804

89,950

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

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

       130        140        150        160        170        180 
SVVNALSQKL ELVIQREGKI HRQIYEHGVP QAPLAVTGET EKTGTMVRFW PSLETFTNVT 

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

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

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

       370        380        390        400        410        420 
LLENPTDAKI 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 LDGATLHTNA SAPALAGEAL EKLVSEYNAT QKMINRMERR 

       610        620        630        640        650        660 
YPKAMLKELI YQPTLTEADL SDEQTVTRWV NALVSELNDK EQHGSQWKFD VHTNAEQNLF 

       670        680        690        700        710        720 
EPIVRVRTHG VDTDYPLDHE FITGGEYRRI CTLGEKLRGL LEEDAFIERG ERRQPVASFE 

       730        740        750        760        770        780 
QALDWLVKES RRGLSIQRYK GLGEMNPEQL WETTMDPESR RMLRVTVKDA IAADQLFTTL 

       790        800 
MGDAVEPRRA FIEENALKAA NIDI

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References

[1]

"Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157."
Jin Q., Yuan Z., Xu J., Wang Y., Shen Y., Lu W., Wang J., Liu H., Yang J., Yang F., Zhang X., Zhang J., Yang G., Wu H., Qu D., Dong J., Sun L., Xue Y.

Yu J.
Nucleic Acids Res. 30:4432-4441(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: 301 / Serotype 2a.

[2]

"Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T."
Wei J., Goldberg M.B., Burland V., Venkatesan M.M., Deng W., Fournier G., Mayhew G.F., Plunkett G. III, Rose D.J., Darling A., Mau B., Perna N.T., Payne S.M., Runyen-Janecky L.J., Zhou S., Schwartz D.C., Blattner F.R.
Infect. Immun. 71:2775-2786(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 700930 / 2457T / Serotype 2a.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE005674 Genomic DNA. Translation: AAN45208.2. AE014073 Genomic DNA. Translation: AAP18989.1.
RefSeq	NP_709501.2. NC_004337.2. NP_839178.1. NC_004741.1.
3D structure databases
ProteinModelPortal	P0AES8.
SMR	P0AES8. Positions 10-392, 402-784.
ModBase	Search...
Protein-protein interaction databases
STRING	198214.SF3765.
Proteomic databases
PaxDb	P0AES8.
PRIDE	P0AES8.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAN45208; AAN45208; SF3765. AAP18989; AAP18989; S4006.
GeneID	1026143. 1080215.
KEGG	sfl:SF3765. sfx:S4006.
PATRIC	18709900. VBIShiFle31049_4359.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0187.
HOGENOM	HOG000075155.
KO	K02470.
OMA	IFETTEF.
ProtClustDB	PRK14939.
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. PS50880. TOPRIM. 1 hit. [Graphical view]
ProtoNet	Search...
Other
BindingDB	P0AES8.

Entry information

Entry name

GYRB_SHIFL

Accession

Primary (citable) accession number: P0AES8
Secondary accession number(s): O08438, P06982

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1988
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 62 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Family and domain databases

Other

Entry information

Relevant documents