RGYR_PYRAB
ID RGYR_PYRAB Reviewed; 1214 AA.
AC Q9UZ86; G8ZKR2;
DT 16-FEB-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 130.
DE RecName: Full=Reverse gyrase {ECO:0000255|HAMAP-Rule:MF_01125};
DE Includes:
DE RecName: Full=Helicase {ECO:0000255|HAMAP-Rule:MF_01125};
DE EC=3.6.4.12 {ECO:0000255|HAMAP-Rule:MF_01125};
DE Includes:
DE RecName: Full=Topoisomerase {ECO:0000255|HAMAP-Rule:MF_01125};
DE EC=5.6.2.2 {ECO:0000255|HAMAP-Rule:MF_01125};
GN Name=rgy {ECO:0000255|HAMAP-Rule:MF_01125}; Synonyms=top-RG;
GN OrderedLocusNames=PYRAB12680; ORFNames=PAB2423;
OS Pyrococcus abyssi (strain GE5 / Orsay).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=272844;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=GE5 / Orsay;
RX PubMed=12622808; DOI=10.1046/j.1365-2958.2003.03381.x;
RA Cohen G.N., Barbe V., Flament D., Galperin M., Heilig R., Lecompte O.,
RA Poch O., Prieur D., Querellou J., Ripp R., Thierry J.-C., Van der Oost J.,
RA Weissenbach J., Zivanovic Y., Forterre P.;
RT "An integrated analysis of the genome of the hyperthermophilic archaeon
RT Pyrococcus abyssi.";
RL Mol. Microbiol. 47:1495-1512(2003).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=GE5 / Orsay;
RX PubMed=22057919; DOI=10.1007/s00284-011-0035-x;
RA Gao J., Wang J.;
RT "Re-annotation of two hyperthermophilic archaea Pyrococcus abyssi GE5 and
RT Pyrococcus furiosus DSM 3638.";
RL Curr. Microbiol. 64:118-129(2012).
CC -!- FUNCTION: Modifies the topological state of DNA by introducing positive
CC supercoils in an ATP-dependent process. It cleaves transiently a single
CC DNA strand and remains covalently bound to the 5' DNA end through a
CC tyrosine residue. May be involved in rewinding the DNA strands in the
CC regions of the chromosome that have opened up to allow transcription or
CC replication. {ECO:0000255|HAMAP-Rule:MF_01125}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.12;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01125};
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_01125};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01125};
CC Note=Binds two Mg(2+) per subunit. {ECO:0000255|HAMAP-Rule:MF_01125};
CC -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_01125}.
CC -!- DOMAIN: Both the DNA unwinding and positive supercoiling activities
CC require the cooperation of both domains. The cooperative action between
CC the helicase-like and the topoisomerase domains is specific. The
CC helicase-like domain probably does not directly unwind DNA but acts
CC more likely by driving ATP-dependent conformational changes within the
CC whole enzyme, functioning more like a protein motor. The 'latch' region
CC of the N-terminal domain plays a regulatory role in the enzyme,
CC repressing topoisomerase activity in the absence of ATP and therefore
CC preventing the enzyme from acting as an ATP-independent relaxing
CC enzyme; it also helps to coordinate nucleotide hydrolysis by the ATPase
CC domain with the supercoiling activity of the topoisomerase domain.
CC {ECO:0000255|HAMAP-Rule:MF_01125}.
CC -!- MISCELLANEOUS: This enzyme is the only unique feature of
CC hyperthermophilic bacteria/archaea discovered so far. It appears to be
CC essential for adaptation to life at high temperatures.
CC -!- SIMILARITY: In the N-terminal section; belongs to the DEAD box helicase
CC family. DDVD subfamily. {ECO:0000255|HAMAP-Rule:MF_01125}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the prokaryotic type
CC I/III topoisomerase family. {ECO:0000255|HAMAP-Rule:MF_01125}.
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DR EMBL; AJ248287; CAB50173.1; -; Genomic_DNA.
DR EMBL; HE613800; CCE70705.1; -; Genomic_DNA.
DR PIR; H75034; H75034.
DR RefSeq; WP_010868381.1; NC_000868.1.
DR AlphaFoldDB; Q9UZ86; -.
DR SMR; Q9UZ86; -.
DR STRING; 272844.PAB2423; -.
DR EnsemblBacteria; CAB50173; CAB50173; PAB2423.
DR GeneID; 1496651; -.
DR KEGG; pab:PAB2423; -.
DR PATRIC; fig|272844.11.peg.1348; -.
DR eggNOG; arCOG01526; Archaea.
DR HOGENOM; CLU_002886_0_0_2; -.
DR OMA; GVATYYG; -.
DR OrthoDB; 1837at2157; -.
DR PhylomeDB; Q9UZ86; -.
DR Proteomes; UP000000810; Chromosome.
DR Proteomes; UP000009139; Chromosome.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003678; F:DNA helicase activity; IEA:UniProtKB-EC.
DR GO; GO:0003918; F:DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity; IEA:UniProtKB-UniRule.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0006265; P:DNA topological change; IEA:UniProtKB-UniRule.
DR GO; GO:0006268; P:DNA unwinding involved in DNA replication; IEA:UniProtKB-UniRule.
DR CDD; cd00186; TOP1Ac; 1.
DR CDD; cd03361; TOPRIM_TopoIA_RevGyr; 1.
DR Gene3D; 1.10.290.10; -; 1.
DR Gene3D; 1.10.460.10; -; 1.
DR Gene3D; 3.40.50.300; -; 3.
DR HAMAP; MF_01125; Reverse_gyrase; 1.
DR InterPro; IPR003593; AAA+_ATPase.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR005736; Reverse_gyrase.
DR InterPro; IPR003601; Topo_IA_2.
DR InterPro; IPR013497; Topo_IA_cen.
DR InterPro; IPR013824; Topo_IA_cen_sub1.
DR InterPro; IPR013826; Topo_IA_cen_sub3.
DR InterPro; IPR023405; Topo_IA_core_domain.
DR InterPro; IPR003602; Topo_IA_DNA-bd_dom.
DR InterPro; IPR006171; TOPRIM_domain.
DR InterPro; IPR034142; TOPRIM_RevGyr.
DR InterPro; IPR040569; Znf_Rg.
DR PANTHER; PTHR43505; PTHR43505; 1.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF01131; Topoisom_bac; 1.
DR Pfam; PF01751; Toprim; 1.
DR Pfam; PF17915; zf_Rg; 1.
DR PRINTS; PR00417; PRTPISMRASEI.
DR SMART; SM00382; AAA; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00437; TOP1Ac; 1.
DR SMART; SM00436; TOP1Bc; 1.
DR SMART; SM00493; TOPRIM; 1.
DR SUPFAM; SSF52540; SSF52540; 2.
DR SUPFAM; SSF56712; SSF56712; 1.
DR TIGRFAMs; TIGR01054; rgy; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS50880; TOPRIM; 1.
PE 3: Inferred from homology;
KW ATP-binding; DNA-binding; Helicase; Hydrolase; Isomerase; Magnesium;
KW Metal-binding; Nucleotide-binding; Repeat; Topoisomerase; Zinc;
KW Zinc-finger.
FT CHAIN 1..1214
FT /note="Reverse gyrase"
FT /id="PRO_0000158087"
FT DOMAIN 93..256
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT DOMAIN 639..802
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT ZN_FING 9..30
FT /note="C4-type 1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT ZN_FING 722..741
FT /note="C4-type 2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT REGION 645..1214
FT /note="Topoisomerase I"
FT MOTIF 213..216
FT /note="DEAD box"
FT ACT_SITE 955
FT /note="For DNA cleavage activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 89
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 106..113
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 645
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_01125"
FT BINDING 771
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_01125"
FT BINDING 771
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 773
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
SQ SEQUENCE 1214 AA; 140013 MW; A2B46AF4343EB620 CRC64;
MKAIYRGMCP NCGGAITDER LAEKNPCEGC LSEPIKAEDY EKLVFAVRNA LKLRGTLKDW
EDLYRLNKEV SEVEDLFKRA TGFRFWSAQR TWVKRILRGK SFSIIAPTGM GKSTFGAFIS
IYFAIKGKRS YIVVPTTPLV VQTVKKIQDM MERAGVNVRL VYYHGNLKKK EKEEALKRIK
DGDFDILVTS SQFLATRFDE LLRDKRFDLI FVDDVDAFLK ASKNIDRSLL LLGFTQEVIN
RAWEVIKLKK QLAKLLQAQG KEKEVEELNK EIEKIEREIE RYRRENNIGI LIVASATGSA
RGDRIKLYRE LLGFEVGSGR SVLRNIVDTY IIPERSIEEE VENLLRKLGK GGLIFVPIDK
GIEFAEELTN YLKSKGFKVE LVSAKNKRGL ELFERGEVDY LVGVATYYGT IVRGLDLPHL
IRFAVFAGVP KFRFSMDLEQ PTIYRVLGLM SEILEFLPQE KREEGEKLYA RLRRLIRNIP
QYELMKIEEA LAEGIELEGF HNHVLDVFKQ AVEFLREVLR DEEVIRRISE NPFLSLKEVE
GKLYIEIPDV RTYIQASGRT SRLFAGGITK GLSVIIVDDQ KVFNGLIRQM RWRFVEFEIK
KFEEINLESV LREIDEDRKK VRLVIEGKIS EQVKDLVKSA LMIVESPNKA RTIASFFGQP
SKRRIGELVA YEVSIGDKML TILASGGHMF DLVTTEGYHG VLILKDDGKP YYVPVYDTIK
RCRDCGHQFV DWEQKGVCPK CGSRNVHDAL ENVKAMRELA LEVDEILIGT DPDTEGEKIA
WDIRNVLSPY TPNIKRIEFH EVTRPAILKA IKEARDINED RVKAQLVRRI EDRWIGFELS
QKLWEVFENR NLSAGRVQTP VLGWIVQRYK EFTESETDFL GLTLENGISI TIENAKGEVK
EVEVKDVVIE EREINPLPPY TTDAMLQDAS RFLGFSATKT MQLAQDLFEL GLCTYHRTDS
IHVSNTGIEI AKEYISEEIG EEYFAPRKWG EEGAHEAIRP TRPIDTGRLI QLIRDGIITL
PRNLTKDHFR LYDLIFRRFI ASQMKPARVL YEKAIISTPF GDVEVEGYIE ILYDGWSRVK
PLPLKQIPKL EKGQKLKVTE IKQWRAPKVS LYTQGDVIAL MKERGIGRPS TYAKIVQTLL
QRGYVIETKG RKKLVPTEKG IKVYQYLVSK YKDLVSEERT RQLEKIMDEI EEAKADYQEV
LRELHEEIKR YIRS
