GYRB_NEIGO
ID GYRB_NEIGO Reviewed; 795 AA.
AC P22118;
DT 01-AUG-1991, integrated into UniProtKB/Swiss-Prot.
DT 22-JUL-2015, sequence version 2.
DT 03-AUG-2022, entry version 111.
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};
OS Neisseria gonorrhoeae.
OC Bacteria; Proteobacteria; Betaproteobacteria; Neisseriales; Neisseriaceae;
OC Neisseria.
OX NCBI_TaxID=485;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=WR302 / MUG116;
RX PubMed=1906260; DOI=10.1128/aac.35.4.622;
RA Stein D.C., Danaher R.J., Cook T.M.;
RT "Characterization of a gyrB mutation responsible for low-level nalidixic
RT acid resistance in Neisseria gonorrhoeae.";
RL Antimicrob. Agents Chemother. 35:622-626(1991).
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA88327.1; Type=Miscellaneous discrepancy; Note=Very strange deletion of 14 amino acids, when compared to other Neisseria gyrB sequences, that looks like a sequencing error.; Evidence={ECO:0000305};
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DR EMBL; M59981; AAA88327.1; ALT_SEQ; Genomic_DNA.
DR PIR; A49794; A49794.
DR AlphaFoldDB; P22118; -.
DR SMR; P22118; -.
DR ChEMBL; CHEMBL2311244; -.
DR DrugCentral; P22118; -.
DR PRIDE; P22118; -.
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; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006265; P:DNA topological change; IEA:UniProtKB-UniRule.
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 3: Inferred from homology;
KW ATP-binding; Cytoplasm; DNA-binding; Isomerase; Magnesium; Metal-binding;
KW Nucleotide-binding; Topoisomerase.
FT CHAIN 1..795
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000145327"
FT DOMAIN 421..536
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 427
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 501
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 501
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 503
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 452
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 455
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
SQ SEQUENCE 795 AA; 88164 MW; 42EC4C958BC909BD CRC64;
MTEQKHEEYG ADSIQVLEGL EAVPKRPGMY IGDTQDGSGL HHMVFEVLDN AIDEALAGHC
DKITVTIHAD HSVSVADNGR GMPTGIHPKE GRSAAEVIMT VLHAGGKFDN NSYKISGGLH
GVGVSVVNAL SDWVTLTIYR DGKEHFVRFV RGETEEPLKI VGDSDKKGTT VRFLAGTETF
GNIEYSFDIL AKRIRELSFL NNGVDIELTD ERDGKHESFA LSGGVAGFVQ YMNRKKTPLH
EKIFYAFGEK DGMSVECAMQ WNDSYQESVQ CFTNNIPQRD GGTHLTALRQ VMTRTINSYI
EANEVAKKAK VETAGDDMRE GLTCVLSVKL PDPKFSSQTK DKLVSGEIGP VVNEVINQAL
TDFLEENPNE AKIITGKIVD AARARQAARK AREITRRKGL MDGLGLPGKL ADCQEKDPAL
SELYLVEGNS AGGSAMQGRD RKFQAILPLK GKILNVEKAR FEKMLASQEV ATLITALGAG
IGKEEFNPEK LRYHRIIIMT DADVDGAHIR TLLLTFFYRQ MPDLVERGYI YIAQPPLYKA
KYGKQERYLK DELEKDQWLL GLALEKAKIV SDGRTIEGAE LADTAKQFLL AKTVIEQESR
FVDELVLRAM LHASPIDLTS SENADKAVAE LSGLLDEKEA ALERIEGHEG HQFIKITRKL
HGNVMVSYIE PKFLNSKAYQ TLTQTAAALK GLVGEGAKLY KGENEYDADS FETALDILMS
VAQKGMSIQR YKGLGEMNPE QLWETTMDPT VRRLLKVRIE DRIADEVFVT LMGDEVEPRR
AFIENNALIA QNIDA
