GYRB_PSEAE
ID GYRB_PSEAE Reviewed; 806 AA.
AC Q9I7C2;
DT 15-MAY-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 138.
DE RecName: Full=DNA gyrase subunit B {ECO:0000255|HAMAP-Rule:MF_01898};
DE EC=5.6.2.2 {ECO:0000255|HAMAP-Rule:MF_01898};
GN Name=gyrB {ECO:0000255|HAMAP-Rule:MF_01898}; OrderedLocusNames=PA0004;
OS Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM
OS 14847 / LMG 12228 / 1C / PRS 101 / PAO1).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=208964;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RX PubMed=10984043; DOI=10.1038/35023079;
RA Stover C.K., Pham X.-Q.T., Erwin A.L., Mizoguchi S.D., Warrener P.,
RA Hickey M.J., Brinkman F.S.L., Hufnagle W.O., Kowalik D.J., Lagrou M.,
RA Garber R.L., Goltry L., Tolentino E., Westbrock-Wadman S., Yuan Y.,
RA Brody L.L., Coulter S.N., Folger K.R., Kas A., Larbig K., Lim R.M.,
RA Smith K.A., Spencer D.H., Wong G.K.-S., Wu Z., Paulsen I.T., Reizer J.,
RA Saier M.H. Jr., Hancock R.E.W., Lory S., Olson M.V.;
RT "Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic
RT pathogen.";
RL Nature 406:959-964(2000).
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 Negative supercoiling favors strand separation, and DNA replication,
CC transcription, recombination and repair, all of which involve strand
CC separation. Also able to catalyze the interconversion of other
CC topological isomers of dsDNA rings, including catenanes and knotted
CC rings. Type II topoisomerases break and join 2 DNA strands
CC simultaneously in an ATP-dependent manner. {ECO:0000255|HAMAP-
CC Rule:MF_01898}.
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_01898};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01898};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01898};
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01898};
CC Note=Binds two Mg(2+) per subunit. The magnesium ions form salt bridges
CC with both the protein and the DNA. Can also accept other divalent metal
CC cations, such as Mn(2+) or Ca(2+). {ECO:0000255|HAMAP-Rule:MF_01898};
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_01898}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01898}.
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_01898}.
CC -!- SIMILARITY: Belongs to the type II topoisomerase GyrB family.
CC {ECO:0000255|HAMAP-Rule:MF_01898}.
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DR EMBL; AE004091; AAG03394.1; -; Genomic_DNA.
DR PIR; H83644; H83644.
DR RefSeq; NP_064724.1; NC_002516.2.
DR RefSeq; WP_003097268.1; NZ_QZGE01000012.1.
DR PDB; 6M1J; X-ray; 1.70 A; A/B=17-221.
DR PDB; 6M1S; X-ray; 2.25 A; A/B=17-221.
DR PDBsum; 6M1J; -.
DR PDBsum; 6M1S; -.
DR AlphaFoldDB; Q9I7C2; -.
DR SMR; Q9I7C2; -.
DR STRING; 287.DR97_2953; -.
DR ChEMBL; CHEMBL3390828; -.
DR PaxDb; Q9I7C2; -.
DR PRIDE; Q9I7C2; -.
DR EnsemblBacteria; AAG03394; AAG03394; PA0004.
DR GeneID; 879230; -.
DR KEGG; pae:PA0004; -.
DR PATRIC; fig|208964.12.peg.4; -.
DR PseudoCAP; PA0004; -.
DR HOGENOM; CLU_006146_4_1_6; -.
DR InParanoid; Q9I7C2; -.
DR OMA; LWETTMH; -.
DR PhylomeDB; Q9I7C2; -.
DR BioCyc; PAER208964:G1FZ6-4-MON; -.
DR Proteomes; UP000002438; 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-KW.
DR GO; GO:0003918; F:DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006265; P:DNA topological change; IBA:GO_Central.
DR GO; GO:0006261; P:DNA-templated DNA replication; IEA:UniProtKB-UniRule.
DR CDD; cd03366; TOPRIM_TopoIIA_GyrB; 1.
DR Gene3D; 3.30.230.10; -; 1.
DR Gene3D; 3.30.565.10; -; 1.
DR Gene3D; 3.40.50.670; -; 2.
DR HAMAP; MF_01898; GyrB; 1.
DR InterPro; IPR002288; DNA_gyrase_B_C.
DR InterPro; IPR011557; GyrB.
DR InterPro; IPR041423; GyrB_insert.
DR InterPro; IPR003594; HATPase_C.
DR InterPro; IPR036890; HATPase_C_sf.
DR InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
DR InterPro; IPR014721; Ribosomal_S5_D2-typ_fold_subgr.
DR InterPro; IPR001241; Topo_IIA.
DR InterPro; IPR013760; Topo_IIA-like_dom_sf.
DR InterPro; IPR013759; Topo_IIA_B_C.
DR InterPro; IPR013506; Topo_IIA_bsu_dom2.
DR InterPro; IPR018522; TopoIIA_CS.
DR InterPro; IPR006171; TOPRIM_domain.
DR InterPro; IPR034160; TOPRIM_GyrB.
DR Pfam; PF00204; DNA_gyraseB; 1.
DR Pfam; PF00986; DNA_gyraseB_C; 1.
DR Pfam; PF18053; GyrB_insert; 1.
DR Pfam; PF02518; HATPase_c; 1.
DR Pfam; PF01751; Toprim; 1.
DR SMART; SM00387; HATPase_c; 1.
DR SMART; SM00433; TOP2c; 1.
DR SUPFAM; SSF54211; SSF54211; 1.
DR SUPFAM; SSF55874; SSF55874; 1.
DR SUPFAM; SSF56719; SSF56719; 1.
DR TIGRFAMs; TIGR01059; gyrB; 1.
DR PROSITE; PS00177; TOPOISOMERASE_II; 1.
DR PROSITE; PS50880; TOPRIM; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Cytoplasm; DNA-binding; Isomerase; Magnesium;
KW Metal-binding; Nucleotide-binding; Reference proteome; Topoisomerase.
FT CHAIN 1..806
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000287820"
FT DOMAIN 420..535
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 426
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 500
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 500
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 502
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 451
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 454
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT HELIX 18..23
FT /evidence="ECO:0007829|PDB:6M1J"
FT HELIX 25..29
FT /evidence="ECO:0007829|PDB:6M1J"
FT STRAND 32..35
FT /evidence="ECO:0007829|PDB:6M1J"
FT HELIX 36..54
FT /evidence="ECO:0007829|PDB:6M1J"
FT STRAND 60..65
FT /evidence="ECO:0007829|PDB:6M1J"
FT STRAND 71..75
FT /evidence="ECO:0007829|PDB:6M1J"
FT TURN 86..88
FT /evidence="ECO:0007829|PDB:6M1J"
FT STRAND 89..91
FT /evidence="ECO:0007829|PDB:6M1S"
FT HELIX 92..98
FT /evidence="ECO:0007829|PDB:6M1J"
FT HELIX 122..127
FT /evidence="ECO:0007829|PDB:6M1J"
FT STRAND 129..138
FT /evidence="ECO:0007829|PDB:6M1J"
FT STRAND 141..148
FT /evidence="ECO:0007829|PDB:6M1J"
FT STRAND 151..154
FT /evidence="ECO:0007829|PDB:6M1J"
FT STRAND 157..161
FT /evidence="ECO:0007829|PDB:6M1J"
FT STRAND 166..173
FT /evidence="ECO:0007829|PDB:6M1J"
FT TURN 175..177
FT /evidence="ECO:0007829|PDB:6M1J"
FT HELIX 185..198
FT /evidence="ECO:0007829|PDB:6M1J"
FT STRAND 203..208
FT /evidence="ECO:0007829|PDB:6M1J"
FT TURN 209..211
FT /evidence="ECO:0007829|PDB:6M1J"
FT STRAND 214..217
FT /evidence="ECO:0007829|PDB:6M1J"
SQ SEQUENCE 806 AA; 90189 MW; DD85D2321F471A57 CRC64;
MSENNTYDSS SIKVLKGLDA VRKRPGMYIG DTDDGTGLHH MVFEVVDNSI DEALAGYCSE
ISITIHTDES ITVRDNGRGI PVDIHKEEGV SAAEVIMTVL HAGGKFDDNT YKVSGGLHGV
GVSVVNALSH ELRLTIRRHN KVWEQVYHHG VPQFPLREVG ETDGSGTEVH FKPSPETFSN
IHFSWDILAK RIRELSFLNS GVGILLRDER TGKEELFKYE GGLKAFVEYL NTNKTAVNEV
FHFNVQREED GVGVEVALQW NDSFNENLLC FTNNIPQRDG GTHLAGFRSA LTRNLNNYIE
AEGLAKKFKI ATTGDDAREG LTAIISVKVP DPKFSSQTKD KLVSSEVKTA VEQEMGKYFA
DFLLENPNEA KAVVGKMIDA ARAREAARKA REMTRRKGAL DIAGLPGKLA DCQEKDPALS
ELYIVEGDSA GGSAKQGRNR RTQAILPLKG KILNVEKARF DKMLSSQEVG TLITALGCGI
GREEYNIDKL RYHNIIIMTD ADVDGSHIRT LLLTFFFRQM PELIERGYIY IAQPPLYKVK
RGKQEQYIKD DQAMEEYMTQ SALEDASLHV NEHAPGLSGA ALEKLVNEYR GVIATLKRLS
RLYPQELTEH FIYLPTVSVD DLANESAMQG WLEKFQARLT AAEKSGLTYK ASLREDRERH
LWLPEVELVA HGLSSYVTFN RDFFASNDYR SVSLLGDQLN SLLEDGAYVQ KGERKRPISA
FKDGLDWLMA EGTKRHSIQR YKGLGEMNPE QLWETTMDPN VRRMLKVTIE DAIAADQIFN
TLMGDAVEPR RDFIESNALA VSNLDV
