ID   RGYR_THEKO              Reviewed;        1711 AA.
AC   Q6F598;
DT   30-AUG-2005, integrated into UniProtKB/Swiss-Prot.
DT   16-AUG-2004, sequence version 1.
DT   03-AUG-2022, entry version 127.
DE   RecName: Full=Reverse gyrase;
DE   Includes:
DE     RecName: Full=Helicase;
DE              EC=3.6.4.12;
DE   Includes:
DE     RecName: Full=Topoisomerase;
DE              EC=5.6.2.2;
DE   Contains:
DE     RecName: Full=Pko r-Gyr intein;
GN   Name=rgy; OrderedLocusNames=TK0470;
OS   Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
OS   (Pyrococcus kodakaraensis (strain KOD1)).
OC   Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC   Thermococcus.
OX   NCBI_TaxID=69014;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX   PubMed=15231817; DOI=10.1128/jb.186.14.4829-4833.2004;
RA   Atomi H., Matsumi R., Imanaka T.;
RT   "Reverse gyrase is not a prerequisite for hyperthermophilic life.";
RL   J. Bacteriol. 186:4829-4833(2004).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX   PubMed=15710748; DOI=10.1101/gr.3003105;
RA   Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.;
RT   "Complete genome sequence of the hyperthermophilic archaeon Thermococcus
RT   kodakaraensis KOD1 and comparison with Pyrococcus genomes.";
RL   Genome Res. 15:352-363(2005).
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 (By similarity). {ECO:0000250}.
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   -!- CATALYTIC ACTIVITY:
CC       Reaction=ATP-dependent breakage, passage and rejoining of double-
CC         stranded DNA.; EC=5.6.2.2;
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC       Note=Binds two Mg(2+) per subunit. {ECO:0000250};
CC   -!- SUBUNIT: Monomer. {ECO:0000250}.
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 (By
CC       similarity). {ECO:0000250}.
CC   -!- PTM: This protein undergoes a protein self splicing that involves a
CC       post-translational excision of the intervening region (intein) followed
CC       by peptide ligation. {ECO:0000250}.
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:0000305}.
CC   -!- SIMILARITY: In the C-terminal section; belongs to the prokaryotic type
CC       I/III topoisomerase family. {ECO:0000305}.
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DR   EMBL; AB117612; BAD26706.1; -; Genomic_DNA.
DR   EMBL; AP006878; BAD84659.1; -; Genomic_DNA.
DR   RefSeq; WP_011249425.1; NC_006624.1.
DR   AlphaFoldDB; Q6F598; -.
DR   SMR; Q6F598; -.
DR   STRING; 69014.TK0470; -.
DR   PRIDE; Q6F598; -.
DR   EnsemblBacteria; BAD84659; BAD84659; TK0470.
DR   GeneID; 3234065; -.
DR   KEGG; tko:TK0470; -.
DR   PATRIC; fig|69014.16.peg.462; -.
DR   eggNOG; arCOG01526; Archaea.
DR   eggNOG; arCOG03151; Archaea.
DR   HOGENOM; CLU_002886_0_0_2; -.
DR   InParanoid; Q6F598; -.
DR   OMA; GVATYYG; -.
DR   OrthoDB; 1837at2157; -.
DR   PhylomeDB; Q6F598; -.
DR   Proteomes; UP000000536; 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:0004519; F:endonuclease activity; IEA:InterPro.
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   GO; GO:0016539; P:intein-mediated protein splicing; IEA:InterPro.
DR   CDD; cd00186; TOP1Ac; 1.
DR   CDD; cd03361; TOPRIM_TopoIA_RevGyr; 1.
DR   Gene3D; 1.10.290.10; -; 2.
DR   Gene3D; 1.10.460.10; -; 2.
DR   Gene3D; 2.70.20.10; -; 2.
DR   Gene3D; 3.10.28.10; -; 1.
DR   Gene3D; 3.40.50.300; -; 3.
DR   HAMAP; MF_01125; Reverse_gyrase; 1.
DR   InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR   InterPro; IPR014001; Helicase_ATP-bd.
DR   InterPro; IPR003586; Hint_dom_C.
DR   InterPro; IPR003587; Hint_dom_N.
DR   InterPro; IPR036844; Hint_dom_sf.
DR   InterPro; IPR027434; Homing_endonucl.
DR   InterPro; IPR030934; Intein_C.
DR   InterPro; IPR004042; Intein_endonuc.
DR   InterPro; IPR006141; Intein_N.
DR   InterPro; IPR004860; LAGLIDADG_2.
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; IPR013825; Topo_IA_cen_sub2.
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; PF14528; LAGLIDADG_3; 1.
DR   Pfam; PF01131; Topoisom_bac; 2.
DR   Pfam; PF01751; Toprim; 1.
DR   Pfam; PF17915; zf_Rg; 1.
DR   PRINTS; PR00417; PRTPISMRASEI.
DR   SMART; SM00487; DEXDc; 1.
DR   SMART; SM00305; HintC; 1.
DR   SMART; SM00306; HintN; 1.
DR   SMART; SM00437; TOP1Ac; 1.
DR   SMART; SM00436; TOP1Bc; 1.
DR   SMART; SM00493; TOPRIM; 1.
DR   SUPFAM; SSF51294; SSF51294; 1.
DR   SUPFAM; SSF52540; SSF52540; 2.
DR   SUPFAM; SSF55608; SSF55608; 1.
DR   SUPFAM; SSF56712; SSF56712; 2.
DR   TIGRFAMs; TIGR01443; intein_Cterm; 1.
DR   TIGRFAMs; TIGR01445; intein_Nterm; 1.
DR   TIGRFAMs; TIGR01054; rgy; 1.
DR   PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR   PROSITE; PS50818; INTEIN_C_TER; 1.
DR   PROSITE; PS50819; INTEIN_ENDONUCLEASE; 1.
DR   PROSITE; PS50817; INTEIN_N_TER; 1.
DR   PROSITE; PS50880; TOPRIM; 1.
PE   3: Inferred from homology;
KW   ATP-binding; Autocatalytic cleavage; DNA-binding; Helicase; Hydrolase;
KW   Isomerase; Magnesium; Metal-binding; Nucleotide-binding; Protein splicing;
KW   Reference proteome; Repeat; Topoisomerase; Zinc; Zinc-finger.
FT   CHAIN           1..960
FT                   /note="Reverse gyrase, 1st part"
FT                   /evidence="ECO:0000255"
FT                   /id="PRO_0000030359"
FT   CHAIN           961..1449
FT                   /note="Pko r-Gyr intein"
FT                   /evidence="ECO:0000255"
FT                   /id="PRO_0000030360"
FT   CHAIN           1450..1711
FT                   /note="Reverse gyrase, 2nd part"
FT                   /evidence="ECO:0000255"
FT                   /id="PRO_0000041880"
FT   DOMAIN          93..256
FT                   /note="Helicase ATP-binding"
FT   DOMAIN          642..805
FT                   /note="Toprim"
FT   DOMAIN          1160..1287
FT                   /note="DOD-type homing endonuclease"
FT   ZN_FING         9..30
FT                   /note="C4-type 1"
FT                   /evidence="ECO:0000250"
FT   ZN_FING         725..744
FT                   /note="C4-type 2"
FT                   /evidence="ECO:0000250"
FT   REGION          648..1711
FT                   /note="Topoisomerase I"
FT   MOTIF           213..216
FT                   /note="DEAD box"
FT   ACT_SITE        1452
FT                   /note="For DNA cleavage activity"
FT                   /evidence="ECO:0000250"
FT   BINDING         89
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   BINDING         106..113
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   BINDING         648
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000250"
FT   BINDING         774
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000250"
FT   BINDING         774
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         776
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   1711 AA;  197560 MW;  73F19BBF5409E127 CRC64;
     MKAVYREMCP NCWGRISDER LVMRNPCEEC LDEPVHADSY FQLVSAVRNA LKLRGTLKEW
     EKIYQLENQT REIEEFFKKA TGFTFWSAQR TWVKRLLKGR SFSIIAPTGM GKSTFGAFMA
     VWHALKGKKS YIVVPTTPLV IQTVRKIEGI MENANADVRL AYYHGNLRKK EKEEMLERIK
     NEDYDILVTS AQWLARNYEE VLKGRHFDFI FVDDVDAFLK ASKNIDRSLY LLGFTDEIIQ
     KAWEIIRLKK QMSRYLNGNS EDRNEKLNGL NREIEKLQRE IEKFKRKNKI GIMIIASATG
     SARGDRIKLY RELLGFEVGS GRSALRNVVD SYLKPTKDIK EHVEELLTRL GKGGLIFVPV
     DQGLGYAEEL ANYLSEKGFK IELVSSKNKK ALEKFENGEA DYLIGSATYY GSLVRGIDLP
     HLIRYAVFTG VPKFRFSIDL ERPTIYRALG LLSEIMDFLS EEDRRQAEKL HARLRRLIRN
     IPQFELLKIE EALAEGLPIE NEFHNHVLGV FRELVEFLRR VLRDEEVLRK LAEDPFISLV
     KEEGKWYIEI PDVRTYIQAT GRTSRLFAGG ITKGLSVLIV DNEKVFNGLV RQMRWRFQEF
     KMVPFEELDL DEILRQIDED REKVRLVMEG KISAKVKDLV RSALMIVESP NKARTIANFF
     GQPSKTRIGD LVAYEISVGD RMLTILASGG HMFDLVTNEG YHGVLIQNEG DMLKFIPVYD
     TLKRCRDCGH QFVDWEKKGV CPRCGSTNVR DALENVIAMR EIAQEVDEIL IATDPDTEGE
     KIAWDIRNVL APYTPNIKRI EFHEVTRPAI MKAIQEARDV NENRVNAQIV RRIEDRWIGF
     ELSQELQRVF ESYNLSAGRV QTPVLGWIIE RYKEFTESEV YFLGLTLENG LQVTIELGKD
     GKDVEPPEYV TVEEVQLEER ELNPAPPYTT DAMLKDASTF LKLSAPETMR LAQDLFEAGL
     CVTPDTLVSL ADGRIMEIKD AVEKSEGNLL SVNGLKPKEA KALKFWEIDW NGPLKVIKLK
     NGHEIKATPD HGLLVMREGK LGWVSAKNVR EGDYVAFAYN TGHRGRDEYT LLKLMIKLGI
     TDVMVELDEE YFNEKVAPIV RERISTSTKY KYLRRRVLPL YLLQEWGLDD YEAHVKSLYR
     QRAGSKPIPN FKLDGRFWYV FGLVLGDGTL RDSKVLISQT PLKDVKSVLE DVFPFLRVFE
     TTNQVGFSNS IIAEVFRRLG ARKGKLHPLV FGLREEYINA MIAGYFDTDG TFSILNDRKG
     PNFRGILTSK RGDVLRMLSV YLYQIGIMNY LRRDERTGVW DLIISNRSLE KFREKIYPYL
     RIRRAQFDEA YSVYRASRRA FEGDLLPVAP VFGKLKFKNG TKNRILKETG IDVWNWLKRP
     EGEIPRDKLS KVLEYAEESP EKEFLKSLVE AGVTWVKVKG VEEELYTGKL YDFTTTTENF
     LSNGAVSHNC TYHRTDSTHV SNTGIEVAKE YITQELGEKY FKPRPWGEEG AHEAIRPTRP
     IDTGRLMQLI RDGIIQLPRN LTRNHYRLYD MIFRRFMTSQ MTPAKILYEK AVINAGVGKA
     ELEGYVEIIE DGWTRLRSPP LRELPKLEKG MKLKVVEAKK WKAPKVSLYT QGDIIALMKE
     RKIGRPSTYA KIVETLMRRG YVVETKGRKK LLPTEKGIKV YHYLVSKYRD LVSEERTREL
     EEIMDRIEEG IEDYIKVLGE LYSEIQRYVS G