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Protein

DNA gyrase subunit A

Gene

gyrA

Organism
Shigella flexneri
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner.UniRule annotation

Catalytic activityi

ATP-dependent breakage, passage and rejoining of double-stranded DNA.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei122 – 1221O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Biological processi

Antibiotic resistance

Keywords - Ligandi

ATP-binding, DNA-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
DNA gyrase subunit AUniRule annotation (EC:5.99.1.3UniRule annotation)
Gene namesi
Name:gyrAUniRule annotation
Ordered Locus Names:SF2311, S2444
OrganismiShigella flexneri
Taxonomic identifieri623 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeShigella
Proteomesi
  • UP000002673 Componenti: Chromosome
  • UP000001006 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 875875DNA gyrase subunit APRO_0000145249Add
BLAST

Proteomic databases

PaxDbiP0AES5.
PRIDEiP0AES5.

Interactioni

Subunit structurei

Heterotetramer, composed of two GyrA and two GyrB chains. In the heterotetramer, GyrA contains the active site tyrosine that forms a transient covalent intermediate with DNA, while GyrB binds cofactors and catalyzes ATP hydrolysis.UniRule annotation

Protein-protein interaction databases

STRINGi198214.SF2311.

Structurei

Secondary structure

1
875
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi15 – 173Combined sources
Helixi24 – 3310Combined sources
Turni37 – 393Combined sources
Helixi43 – 5412Combined sources
Helixi66 – 7611Combined sources
Helixi84 – 918Combined sources
Turni95 – 973Combined sources
Beta strandi102 – 1076Combined sources
Turni120 – 1223Combined sources
Beta strandi124 – 1274Combined sources
Helixi129 – 1346Combined sources
Turni135 – 1395Combined sources
Beta strandi145 – 1473Combined sources
Beta strandi151 – 1588Combined sources
Helixi165 – 1695Combined sources
Turni174 – 1774Combined sources
Helixi187 – 19913Combined sources
Helixi205 – 2117Combined sources
Helixi227 – 2359Combined sources
Beta strandi236 – 2438Combined sources
Beta strandi245 – 2506Combined sources
Turni252 – 2543Combined sources
Beta strandi257 – 2637Combined sources
Helixi270 – 28213Combined sources
Beta strandi288 – 2947Combined sources
Beta strandi303 – 3075Combined sources
Helixi313 – 3219Combined sources
Beta strandi327 – 3337Combined sources
Beta strandi335 – 3384Combined sources
Beta strandi341 – 3444Combined sources
Helixi347 – 38842Combined sources
Helixi390 – 39910Combined sources
Helixi403 – 41210Combined sources
Turni418 – 4203Combined sources
Helixi421 – 4244Combined sources
Beta strandi441 – 4499Combined sources
Helixi452 – 4609Combined sources
Helixi463 – 4664Combined sources
Helixi469 – 49224Combined sources
Helixi495 – 51319Combined sources
Beta strandi519 – 5213Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2Y3PX-ray2.62A/B2-523[»]
ProteinModelPortaliP0AES5.
SMRiP0AES5. Positions 13-522, 535-841.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AES5.

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi560 – 5667GyrA-boxUniRule annotation

Sequence similaritiesi

Belongs to the type II topoisomerase GyrA/ParC subunit family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C24. Bacteria.
COG0188. LUCA.
HOGENOMiHOG000076278.
KOiK02469.
OMAiETVDWVP.
OrthoDBiEOG661H5V.

Family and domain databases

Gene3Di1.10.268.10. 1 hit.
3.30.1360.40. 1 hit.
3.90.199.10. 1 hit.
HAMAPiMF_01897. GyrA.
InterProiIPR024946. Arg_repress_C-like.
IPR005743. GyrA.
IPR006691. GyrA/parC_pinwhl.
IPR013760. Topo_IIA-like_dom.
IPR002205. Topo_IIA_A/C.
IPR013758. Topo_IIA_A/C_ab.
IPR013757. Topo_IIA_A_a.
[Graphical view]
PfamiPF03989. DNA_gyraseA_C. 6 hits.
PF00521. DNA_topoisoIV. 1 hit.
[Graphical view]
SMARTiSM00434. TOP4c. 1 hit.
[Graphical view]
SUPFAMiSSF56719. SSF56719. 1 hit.
TIGRFAMsiTIGR01063. gyrA. 1 hit.

Sequencei

Sequence statusi: Complete.

P0AES5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSDLAREITP VNIEEELKSS YLDYAMSVIV GRALPDVRDG LKPVHRRVLY
60 70 80 90 100
AMNVLGNDWN KAYKKSARVV GDVIGKYHPH GDSAVYDTIV RMAQPFSLRY
110 120 130 140 150
MLVDGQGNFG SIDGDSAAAM RYTEIRLAKI AHELMADLEK ETVDFVDNYD
160 170 180 190 200
GTEKIPDVMP TKIPNLLVNG SSGIAVGMAT NIPPHNLTEV INGCLAYIDD
210 220 230 240 250
EDISIEGLME HIPGPDFPTA AIINGRRGIE EAYRTGRGKV YIRARAEVEV
260 270 280 290 300
DAKTGRETII VHEIPYQVNK ARLIEKIAEL VKEKRVEGIS ALRDESDKDG
310 320 330 340 350
MRIVIEVKRD AVGEVVLNNL YSQTQLQVSF GINMVALHHG QPKIMNLKDI
360 370 380 390 400
IAAFVRHRRE VVTRRTIFEL RKARDRAHIL EALAVALANI DPIIELIRHA
410 420 430 440 450
PTPAEAKTAL VANPWQLGNV AAMLERAGDD AARPEWLEPE FGVRDGLYYL
460 470 480 490 500
TEQQAQAILD LRLQKLTGLE HEKLLDEYKE LLDQIAELLR ILGSADRLME
510 520 530 540 550
VIREELELVR EQFGDKRRTE ITANSADINL EDLITQEDVV VTLSHQGYVK
560 570 580 590 600
YQPLSEYEAQ RRGGKGKSAA RIKEEDFIDR LLVANTHDHI LCFSSRGRVY
610 620 630 640 650
SMKVYQLPEA TRGARGRPIV NLLPLEQDER ITAILPVTEF EEGVKVFMAT
660 670 680 690 700
ANGTVKKTVL TEFNRLRTAG KVAIKLVDGD ELIGVDLTSG EDEVMLFSAE
710 720 730 740 750
GKVVRFKESS VRAMGCNTTG VRGIRLGEGD KVVSLIVPRG DGAILTATQN
760 770 780 790 800
GYGKRTAVAE YPTKSRATKG VISIKVTERN GLVVGAVQVD DCDQIMMITD
810 820 830 840 850
AGTLVRTRVS EISIVGRNTQ GVILIRTAED ENVVGLQRVA EPVDEEDLDT
860 870
IDGSAAEGDD EIAPEVDVDD EPEEE
Length:875
Mass (Da):96,964
Last modified:December 20, 2005 - v1
Checksum:i3FD5BD52A5969069
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE005674 Genomic DNA. Translation: AAN43827.1.
AE014073 Genomic DNA. Translation: AAP17645.1.
RefSeqiNP_708120.1. NC_004337.2.
WP_001281242.1. NZ_LM651928.1.

Genome annotation databases

EnsemblBacteriaiAAN43827; AAN43827; SF2311.
AAP17645; AAP17645; S2444.
GeneIDi1027274.
KEGGisfl:SF2311.
sfx:S2444.
PATRICi18706469. VBIShiFle31049_2710.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE005674 Genomic DNA. Translation: AAN43827.1.
AE014073 Genomic DNA. Translation: AAP17645.1.
RefSeqiNP_708120.1. NC_004337.2.
WP_001281242.1. NZ_LM651928.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2Y3PX-ray2.62A/B2-523[»]
ProteinModelPortaliP0AES5.
SMRiP0AES5. Positions 13-522, 535-841.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi198214.SF2311.

Proteomic databases

PaxDbiP0AES5.
PRIDEiP0AES5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAN43827; AAN43827; SF2311.
AAP17645; AAP17645; S2444.
GeneIDi1027274.
KEGGisfl:SF2311.
sfx:S2444.
PATRICi18706469. VBIShiFle31049_2710.

Phylogenomic databases

eggNOGiENOG4105C24. Bacteria.
COG0188. LUCA.
HOGENOMiHOG000076278.
KOiK02469.
OMAiETVDWVP.
OrthoDBiEOG661H5V.

Miscellaneous databases

EvolutionaryTraceiP0AES5.

Family and domain databases

Gene3Di1.10.268.10. 1 hit.
3.30.1360.40. 1 hit.
3.90.199.10. 1 hit.
HAMAPiMF_01897. GyrA.
InterProiIPR024946. Arg_repress_C-like.
IPR005743. GyrA.
IPR006691. GyrA/parC_pinwhl.
IPR013760. Topo_IIA-like_dom.
IPR002205. Topo_IIA_A/C.
IPR013758. Topo_IIA_A/C_ab.
IPR013757. Topo_IIA_A_a.
[Graphical view]
PfamiPF03989. DNA_gyraseA_C. 6 hits.
PF00521. DNA_topoisoIV. 1 hit.
[Graphical view]
SMARTiSM00434. TOP4c. 1 hit.
[Graphical view]
SUPFAMiSSF56719. SSF56719. 1 hit.
TIGRFAMsiTIGR01063. gyrA. 1 hit.
ProtoNetiSearch...

Publicationsi

  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.
    , Zhao A., Gao Y., Zhu J., Kan B., Ding K., Chen S., Cheng H., Yao Z., He B., Chen R., Ma D., Qiang B., Wen Y., Hou 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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700930 / 2457T / Serotype 2a.

Entry informationi

Entry nameiGYRA_SHIFL
AccessioniPrimary (citable) accession number: P0AES5
Secondary accession number(s): P09097
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: December 20, 2005
Last modified: June 8, 2016
This is version 79 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Few gyrases are as efficient as E.coli at forming negative supercoils. Not all organisms have 2 type II topoisomerases; in organisms with a single type II topoisomerase this enzyme also has to decatenate newly replicated chromosomes.UniRule annotation

Keywords - Technical termi

3D-structure, Complete proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.