GYRA_BORBU
ID GYRA_BORBU Reviewed; 810 AA.
AC O51396; Q44931;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1998, sequence version 1.
DT 03-AUG-2022, entry version 147.
DE RecName: Full=DNA gyrase subunit A {ECO:0000255|HAMAP-Rule:MF_01897};
DE EC=5.6.2.2 {ECO:0000255|HAMAP-Rule:MF_01897};
GN Name=gyrA {ECO:0000255|HAMAP-Rule:MF_01897}; OrderedLocusNames=BB_0435;
OS Borreliella burgdorferi (strain ATCC 35210 / DSM 4680 / CIP 102532 / B31)
OS (Borrelia burgdorferi).
OC Bacteria; Spirochaetes; Spirochaetales; Borreliaceae; Borreliella.
OX NCBI_TaxID=224326;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 35210 / DSM 4680 / CIP 102532 / B31;
RX PubMed=9403685; DOI=10.1038/37551;
RA Fraser C.M., Casjens S., Huang W.M., Sutton G.G., Clayton R.A.,
RA Lathigra R., White O., Ketchum K.A., Dodson R.J., Hickey E.K., Gwinn M.L.,
RA Dougherty B.A., Tomb J.-F., Fleischmann R.D., Richardson D.L.,
RA Peterson J.D., Kerlavage A.R., Quackenbush J., Salzberg S.L., Hanson M.,
RA van Vugt R., Palmer N., Adams M.D., Gocayne J.D., Weidman J.F.,
RA Utterback T.R., Watthey L., McDonald L.A., Artiach P., Bowman C.,
RA Garland S.A., Fujii C., Cotton M.D., Horst K., Roberts K.M., Hatch B.,
RA Smith H.O., Venter J.C.;
RT "Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi.";
RL Nature 390:580-586(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 450-545.
RC STRAIN=212;
RX PubMed=1490605; DOI=10.1016/0378-1097(92)90034-l;
RA Old I.G., Macdougall J.H., Saint-Girons I., Davidson B.E.;
RT "Mapping of genes on the linear chromosome of the bacterium Borrelia
RT burgdorferi: possible locations for its origin of replication.";
RL FEMS Microbiol. Lett. 78:245-250(1992).
RN [3]
RP FUNCTION, AND DOMAIN.
RC STRAIN=ATCC 35210 / DSM 4680 / CIP 102532 / B31;
RX PubMed=15897198; DOI=10.1074/jbc.m502838200;
RA Ruthenburg A.J., Graybosch D.M., Huetsch J.C., Verdine G.L.;
RT "A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal
RT domain imparts unidirectional supercoiling bias.";
RL J. Biol. Chem. 280:26177-26184(2005).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) OF 499-810, DOMAIN, AND DNA-BINDING.
RC STRAIN=ATCC 35210 / DSM 4680 / CIP 102532 / B31;
RX PubMed=15123801; DOI=10.1073/pnas.0401595101;
RA Corbett K.D., Shultzaberger R.K., Berger J.M.;
RT "The C-terminal domain of DNA gyrase A adopts a DNA-bending beta-pinwheel
RT fold.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:7293-7298(2004).
CC -!- FUNCTION: A type II topoisomerase that negatively supercoils closed
CC circular double-stranded (ds) DNA in an ATP-dependent manner to
CC modulate DNA topology and maintain chromosomes in an underwound state
CC (PubMed:15897198). Negative supercoiling favors strand separation, and
CC DNA replication, transcription, recombination and repair, all of which
CC involve strand separation. Also able to catalyze the interconversion of
CC other topological isomers of dsDNA rings, including catenanes and
CC knotted rings. Type II topoisomerases break and join 2 DNA strands
CC simultaneously in an ATP-dependent manner. {ECO:0000255|HAMAP-
CC Rule:MF_01897, ECO:0000269|PubMed:15897198}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP-dependent breakage, passage and rejoining of double-
CC stranded DNA.; EC=5.6.2.2; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01897};
CC -!- SUBUNIT: Heterotetramer, composed of two GyrA and two GyrB chains. In
CC the heterotetramer, GyrA contains the active site tyrosine that forms a
CC transient covalent intermediate with DNA, while GyrB binds cofactors
CC and catalyzes ATP hydrolysis. {ECO:0000255|HAMAP-Rule:MF_01897}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01897}.
CC -!- DOMAIN: The C-terminal domain (CTD, residues 499-810) contains 6
CC tandemly repeated subdomains known as blades, each of which is composed
CC of a 4-stranded antiparallel beta-sheet. The blades form a flat,
CC toroidal beta-pinwheel fold, to which DNA probably binds, inducing mild
CC positive superhelicity (about 0.3 links/protein) (PubMed:15897198,
CC PubMed:15123801). {ECO:0000269|PubMed:15123801,
CC ECO:0000269|PubMed:15897198}.
CC -!- MISCELLANEOUS: Few gyrases are as efficient as E.coli at forming
CC negative supercoils. Not all organisms have 2 type II topoisomerases;
CC in organisms with a single type II topoisomerase this enzyme also has
CC to decatenate newly replicated chromosomes. {ECO:0000255|HAMAP-
CC Rule:MF_01897}.
CC -!- SIMILARITY: Belongs to the type II topoisomerase GyrA/ParC subunit
CC family. {ECO:0000255|HAMAP-Rule:MF_01897}.
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DR EMBL; AE000783; AAC66803.1; -; Genomic_DNA.
DR EMBL; Z12165; CAA78157.1; -; Genomic_DNA.
DR PIR; B70154; B70154.
DR RefSeq; NP_212569.1; NC_001318.1.
DR RefSeq; WP_002656784.1; NC_001318.1.
DR PDB; 1SUU; X-ray; 1.75 A; A=499-810.
DR PDBsum; 1SUU; -.
DR AlphaFoldDB; O51396; -.
DR SMR; O51396; -.
DR STRING; 224326.BB_0435; -.
DR PRIDE; O51396; -.
DR EnsemblBacteria; AAC66803; AAC66803; BB_0435.
DR GeneID; 56567866; -.
DR KEGG; bbu:BB_0435; -.
DR PATRIC; fig|224326.49.peg.826; -.
DR HOGENOM; CLU_002977_4_1_12; -.
DR OMA; THHWLLF; -.
DR EvolutionaryTrace; O51396; -.
DR Proteomes; UP000001807; Chromosome.
DR GO; GO:0005694; C:chromosome; IEA:InterPro.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0034335; F:DNA negative supercoiling activity; IEA:UniProt.
DR GO; GO:0006265; P:DNA topological change; IEA:UniProtKB-UniRule.
DR GO; GO:0006261; P:DNA-templated DNA replication; IEA:UniProtKB-UniRule.
DR GO; GO:0046677; P:response to antibiotic; IEA:UniProtKB-KW.
DR CDD; cd00187; TOP4c; 1.
DR Gene3D; 1.10.268.10; -; 1.
DR Gene3D; 2.120.10.90; -; 1.
DR Gene3D; 3.90.199.10; -; 1.
DR HAMAP; MF_01897; GyrA; 1.
DR InterPro; IPR005743; GyrA.
DR InterPro; IPR006691; GyrA/parC_rep.
DR InterPro; IPR035516; Gyrase/topoIV_suA_C.
DR InterPro; IPR013760; Topo_IIA-like_dom_sf.
DR InterPro; IPR013758; Topo_IIA_A/C_ab.
DR InterPro; IPR013757; Topo_IIA_A_a_sf.
DR InterPro; IPR002205; Topo_IIA_dom_A.
DR Pfam; PF03989; DNA_gyraseA_C; 6.
DR Pfam; PF00521; DNA_topoisoIV; 1.
DR SMART; SM00434; TOP4c; 1.
DR SUPFAM; SSF101904; SSF101904; 1.
DR SUPFAM; SSF56719; SSF56719; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Antibiotic resistance; ATP-binding; Cytoplasm; DNA-binding;
KW Isomerase; Nucleotide-binding; Reference proteome; Topoisomerase.
FT CHAIN 1..810
FT /note="DNA gyrase subunit A"
FT /id="PRO_0000145222"
FT REGION 499..810
FT /note="C-terminal domain"
FT /evidence="ECO:0000303|PubMed:15897198"
FT MOTIF 529..535
FT /note="GyrA-box"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01897"
FT ACT_SITE 124
FT /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01897"
FT CONFLICT 469..472
FT /note="IREE -> YKRR (in Ref. 2; CAA78157)"
FT /evidence="ECO:0000305"
FT CONFLICT 539
FT /note="F -> Y (in Ref. 2; CAA78157)"
FT /evidence="ECO:0000305"
FT STRAND 507..513
FT /evidence="ECO:0007829|PDB:1SUU"
FT STRAND 517..522
FT /evidence="ECO:0007829|PDB:1SUU"
FT HELIX 523..525
FT /evidence="ECO:0007829|PDB:1SUU"
FT STRAND 547..554
FT /evidence="ECO:0007829|PDB:1SUU"
FT STRAND 558..563
FT /evidence="ECO:0007829|PDB:1SUU"
FT STRAND 566..572
FT /evidence="ECO:0007829|PDB:1SUU"
FT HELIX 573..575
FT /evidence="ECO:0007829|PDB:1SUU"
FT HELIX 588..590
FT /evidence="ECO:0007829|PDB:1SUU"
FT STRAND 600..607
FT /evidence="ECO:0007829|PDB:1SUU"
FT STRAND 614..619
FT /evidence="ECO:0007829|PDB:1SUU"
FT STRAND 622..628
FT /evidence="ECO:0007829|PDB:1SUU"
FT HELIX 629..632
FT /evidence="ECO:0007829|PDB:1SUU"
FT STRAND 651..657
FT /evidence="ECO:0007829|PDB:1SUU"
FT STRAND 662..667
FT /evidence="ECO:0007829|PDB:1SUU"
FT STRAND 670..676
FT /evidence="ECO:0007829|PDB:1SUU"
FT HELIX 677..679
FT /evidence="ECO:0007829|PDB:1SUU"
FT STRAND 701..706
FT /evidence="ECO:0007829|PDB:1SUU"
FT STRAND 711..717
FT /evidence="ECO:0007829|PDB:1SUU"
FT STRAND 720..726
FT /evidence="ECO:0007829|PDB:1SUU"
FT HELIX 727..729
FT /evidence="ECO:0007829|PDB:1SUU"
FT TURN 748..750
FT /evidence="ECO:0007829|PDB:1SUU"
FT STRAND 752..759
FT /evidence="ECO:0007829|PDB:1SUU"
FT STRAND 764..769
FT /evidence="ECO:0007829|PDB:1SUU"
FT STRAND 773..778
FT /evidence="ECO:0007829|PDB:1SUU"
FT HELIX 779..781
FT /evidence="ECO:0007829|PDB:1SUU"
FT STRAND 802..807
FT /evidence="ECO:0007829|PDB:1SUU"
SQ SEQUENCE 810 AA; 91379 MW; 395F3930F0EF1650 CRC64;
MAVGENKEQI LNVRIEDEIK TSYLNYAMSV IVSRALPDVR DGLKPVHRRI LYSMYEMGLR
SDKAFKKAGR IVGDVLGKYH PHGDQSIYDA LVRLAQDFSL RYPVIRGQGN FGSIDGDPPA
AMRYTEAKME KITEYIVKDI DKETVNFKSN YDDSLSEPEI MPSSFPFLLV NGSSGIAVGM
ATNMAPHNLR EICDAIVYML DNENASIFDL LKIVKGPDFP TFGEIVYNDN LIKAYKTGKG
SVVIRARYHI EERAEDRNAI IVTEIPYTVN KSALLMKVAL LAKEEKLEGL LDIRDESDRE
GIRIVLEVKR GFDPHVIMNL LYEYTEFKKH FSINNLALVN GIPKQLNLEE LLFEFIEHRK
NIIERRIEFD LRKAKEKAHV LEGLNIALNN IDEVIKIIKS SKLAKDARER LVSNFGLSEI
QANSVLDMRL QKLTALEIFK LEEELNILLS LIKDYEDILL NPVRIINIIR EETINLGLKF
GDERRTKIIY DEEVLKTSMS DLMQKENIVV MLTKKGFLKR LSQNEYKLQG TGGKGLSSFD
LNDGDEIVIA LCVNTHDYLF MISNEGKLYL INAYEIKDSS RASKGQNISE LINLGDQEEI
LTIKNSKDLT DDAYLLLTTA SGKIARFEST DFKAVKSRGV IVIKLNDKDF VTSAEIVFKD
EKVICLSKKG SAFIFNSRDV RLTNRGTQGV CGMKLKEGDL FVKVLSVKEN PYLLIVSENG
YGKRLNMSKI SELKRGATGY TSYKKSDKKA GSVVDAIAVS EDDEILLVSK RSKALRTVAG
KVSEQGKDAR GIQVLFLDND SLVSVSKFIK
