TOP4B_AQUAE
ID TOP4B_AQUAE Reviewed; 792 AA.
AC O67137;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 137.
DE RecName: Full=Type 2 topoisomerase subunit B {ECO:0000303|PubMed:21076033};
DE EC=5.6.2.2 {ECO:0000255|HAMAP-Rule:MF_01898, ECO:0000269|PubMed:21076033};
DE AltName: Full=DNA gyrase subunit B;
GN Name=gyrB {ECO:0000255|HAMAP-Rule:MF_01898}; OrderedLocusNames=aq_1026;
OS Aquifex aeolicus (strain VF5).
OC Bacteria; Aquificae; Aquificales; Aquificaceae; Aquifex.
OX NCBI_TaxID=224324;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=VF5;
RX PubMed=9537320; DOI=10.1038/32831;
RA Deckert G., Warren P.V., Gaasterland T., Young W.G., Lenox A.L.,
RA Graham D.E., Overbeek R., Snead M.A., Keller M., Aujay M., Huber R.,
RA Feldman R.A., Short J.M., Olsen G.J., Swanson R.V.;
RT "The complete genome of the hyperthermophilic bacterium Aquifex aeolicus.";
RL Nature 392:353-358(1998).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RX PubMed=21076033; DOI=10.1073/pnas.1012938107;
RA Tretter E.M., Lerman J.C., Berger J.M.;
RT "A naturally chimeric type IIA topoisomerase in Aquifex aeolicus highlights
RT an evolutionary path for the emergence of functional paralogs.";
RL Proc. Natl. Acad. Sci. U.S.A. 107:22055-22059(2010).
CC -!- FUNCTION: A type II topoisomerase. Despite its similarity to DNA
CC gyrase, this enzyme is not able to supercoil DNA, and instead acts like
CC topoisomerase IV. Relaxes both positively and negatively supercoiled
CC DNA in an ATP-dependent fashion, decatenates interlocked circles. If
CC this subunit is reconstituted with GyrA from E.coli the hybrid enzyme
CC supercoils relaxed plasmid DNA; if paired with E.coli ParC supercoiling
CC is not restored. This the first bacteria shown to not contain DNA
CC gyrase, although it has 2 copies of a reverse gyrase that introduces
CC positive supercoils. Type II topoisomerases break and join 2 DNA
CC strands simultaneously in an ATP-dependent manner (PubMed:21076033).
CC {ECO:0000269|PubMed:21076033}.
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-Rule:MF_01898,
CC ECO:0000269|PubMed:21076033};
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 -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Temperature dependence:
CC Optimum temperature is 70 degrees Celsius, active between 37 and 90
CC degrees Celsius. {ECO:0000269|PubMed:21076033};
CC -!- SUBUNIT: Heterotetramer, composed of two GyrA and two GyrB chains. In
CC the heterotetramer, 'GyrA' contains the active site tyrosine that forms
CC a transient covalent intermediate with DNA, while 'GyrB' binds
CC cofactors and catalyzes ATP hydrolysis (PubMed:21076033).
CC {ECO:0000255|HAMAP-Rule:MF_01898, ECO:0000305|PubMed:21076033}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-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; AE000657; AAC07098.1; -; Genomic_DNA.
DR PIR; F70388; F70388.
DR RefSeq; NP_213700.1; NC_000918.1.
DR RefSeq; WP_010880638.1; NC_000918.1.
DR AlphaFoldDB; O67137; -.
DR SMR; O67137; -.
DR STRING; 224324.aq_1026; -.
DR EnsemblBacteria; AAC07098; AAC07098; aq_1026.
DR KEGG; aae:aq_1026; -.
DR PATRIC; fig|224324.8.peg.802; -.
DR eggNOG; COG0187; Bacteria.
DR HOGENOM; CLU_006146_0_1_0; -.
DR InParanoid; O67137; -.
DR OMA; LWETTMH; -.
DR OrthoDB; 205481at2; -.
DR Proteomes; UP000000798; Chromosome.
DR GO; GO:0005694; C:chromosome; IEA:InterPro.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0009330; C:DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex; IDA:UniProtKB.
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; 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; 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; 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 ATP-binding; Cytoplasm; DNA-binding; Isomerase; Magnesium; Metal-binding;
KW Nucleotide-binding; Reference proteome; Topoisomerase.
FT CHAIN 1..792
FT /note="Type 2 topoisomerase subunit B"
FT /id="PRO_0000145289"
FT DOMAIN 423..537
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 429
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 502
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 502
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 504
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
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 SITE 457
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
SQ SEQUENCE 792 AA; 90530 MW; 07DC02DF293FF9F3 CRC64;
MKKRQSQTPQ EYTAEAIKAV SGLEHVRLRP AMYIGDIGER GLHHLIWEIL DNAVDEAVAG
YARNISVTIH RDNSVTVEDD GRGIPVDIHP ETGKPAVEMV FTMLGAGGKF EKKVYTYSGG
LHGVGASVVN ALSEWLIVEV YRDGKIYRMA FKRGEVVEPL HVVGETKKRG TKVSFKPDPE
IFETTEIKFD IVEKRVRELA YLNPEVKFEL TDERLGKHLI YKFDRGIEEL VKYLNEGKEP
LFKDIIRIQG EKEGVIVDIA FQYVKDYKER IESFVNNIKT VEGGTHVTGF RSGLSKAVIR
MAQGLKLAKE LKKSFTGEDV REGLTAVVAC KVPNPQFEGQ TKTKLGNQNV KQIVESITYD
FLTSYFEKKR DVLKAIVEKA IEAALAREAA KKAKELVRRK SPLEEGVLPG KLADCSETDP
SKCEIFLVEG DSAGGSAKQA RDRRYQAILP LRGKIINVEK ARIDKVLSND EIKAIVSALG
CGIGEDLDLK KLRYHKIILM TDADVDGSHI RTLLLTFFYR FMPKLVEEGY VYIAEPPLYR
VKKGKKEIYI KDDKEFEHFL LNEIREKGRL VDAREKEFKG EELVRLLIDL KDYEDAYRAL
VKSKGENLVN FLLTHRVREE DLRNPARVKE ITHLMEEELG DYRVDTKYNE LEGAYDIIFY
DDKLGTKTII DVNFLSSLSY REVLEGIHLH LPVQVFFENK KVEINSLGEI YDKFMDFARS
GMEVQRYKGL GEMNPEQLWE TTMNPKTRRL KKVKIEDAAE ADRIFTILMG EQVEPRREFI
EAYAKEVKHL DV
