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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)DescriptionActionsGraphical viewLength
Active sitei122O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation1

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeShigella
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)DescriptionActionsGraphical viewLength
ChainiPRO_00001452491 – 875DNA gyrase subunit AAdd BLAST875

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

1875
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi15 – 17Combined sources3
Helixi24 – 33Combined sources10
Turni37 – 39Combined sources3
Helixi43 – 54Combined sources12
Helixi66 – 76Combined sources11
Helixi84 – 91Combined sources8
Turni95 – 97Combined sources3
Beta strandi102 – 107Combined sources6
Turni120 – 122Combined sources3
Beta strandi124 – 127Combined sources4
Helixi129 – 134Combined sources6
Turni135 – 139Combined sources5
Beta strandi145 – 147Combined sources3
Beta strandi151 – 158Combined sources8
Helixi165 – 169Combined sources5
Turni174 – 177Combined sources4
Helixi187 – 199Combined sources13
Helixi205 – 211Combined sources7
Helixi227 – 235Combined sources9
Beta strandi236 – 243Combined sources8
Beta strandi245 – 250Combined sources6
Turni252 – 254Combined sources3
Beta strandi257 – 263Combined sources7
Helixi270 – 282Combined sources13
Beta strandi288 – 294Combined sources7
Beta strandi303 – 307Combined sources5
Helixi313 – 321Combined sources9
Beta strandi327 – 333Combined sources7
Beta strandi335 – 338Combined sources4
Beta strandi341 – 344Combined sources4
Helixi347 – 388Combined sources42
Helixi390 – 399Combined sources10
Helixi403 – 412Combined sources10
Turni418 – 420Combined sources3
Helixi421 – 424Combined sources4
Beta strandi441 – 449Combined sources9
Helixi452 – 460Combined sources9
Helixi463 – 466Combined sources4
Helixi469 – 492Combined sources24
Helixi495 – 513Combined sources19
Beta strandi519 – 521Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2Y3PX-ray2.62A/B2-523[»]
ProteinModelPortaliP0AES5.
SMRiP0AES5.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AES5.

Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi560 – 566GyrA-boxUniRule annotation7

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105C24. Bacteria.
COG0188. LUCA.
HOGENOMiHOG000076278.
KOiK02469.
OMAiEMKSAYI.

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. 1 hit.
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.

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.
sft:NCTC1_02543.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2Y3PX-ray2.62A/B2-523[»]
ProteinModelPortaliP0AES5.
SMRiP0AES5.
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.
sft:NCTC1_02543.
sfx:S2444.
PATRICi18706469. VBIShiFle31049_2710.

Phylogenomic databases

eggNOGiENOG4105C24. Bacteria.
COG0188. LUCA.
HOGENOMiHOG000076278.
KOiK02469.
OMAiEMKSAYI.

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. 1 hit.
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.
ProtoNetiSearch...

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: November 2, 2016
This is version 83 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.