ID   RGYR_PYRHO              Reviewed;        1624 AA.
AC   O58530;
DT   16-FEB-2004, integrated into UniProtKB/Swiss-Prot.
DT   01-AUG-1998, sequence version 1.
DT   03-AUG-2022, entry version 140.
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=Pho r-Gyr intein;
GN   Name=rgy; OrderedLocusNames=PH0800;
OS   Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC
OS   100139 / OT-3).
OC   Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC   Pyrococcus.
OX   NCBI_TaxID=70601;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX   PubMed=9679194; DOI=10.1093/dnares/5.2.55;
RA   Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S.,
RA   Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K.,
RA   Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T., Tanaka T.,
RA   Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T.,
RA   Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H.;
RT   "Complete sequence and gene organization of the genome of a hyper-
RT   thermophilic archaebacterium, Pyrococcus horikoshii OT3.";
RL   DNA Res. 5:55-76(1998).
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:0000305}.
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; BA000001; BAA29893.1; -; Genomic_DNA.
DR   PIR; C71129; C71129.
DR   RefSeq; WP_010884895.1; NC_000961.1.
DR   AlphaFoldDB; O58530; -.
DR   SMR; O58530; -.
DR   STRING; 70601.3257210; -.
DR   EnsemblBacteria; BAA29893; BAA29893; BAA29893.
DR   GeneID; 1443130; -.
DR   KEGG; pho:PH0800; -.
DR   eggNOG; arCOG01526; Archaea.
DR   eggNOG; arCOG03151; Archaea.
DR   OMA; GVATYYG; -.
DR   OrthoDB; 1837at2157; -.
DR   Proteomes; UP000000752; 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; -; 1.
DR   Gene3D; 1.10.460.10; -; 2.
DR   Gene3D; 2.70.20.10; -; 1.
DR   Gene3D; 3.10.28.10; -; 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; 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; SM00382; AAA; 1.
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   Repeat; Topoisomerase; Zinc; Zinc-finger.
FT   CHAIN           1..953
FT                   /note="Reverse gyrase, 1st part"
FT                   /evidence="ECO:0000255"
FT                   /id="PRO_0000030356"
FT   CHAIN           954..1363
FT                   /note="Pho r-Gyr intein"
FT                   /evidence="ECO:0000255"
FT                   /id="PRO_0000030357"
FT   CHAIN           1364..1624
FT                   /note="Reverse gyrase, 2nd part"
FT                   /evidence="ECO:0000255"
FT                   /id="PRO_0000030358"
FT   DOMAIN          93..256
FT                   /note="Helicase ATP-binding"
FT   DOMAIN          640..803
FT                   /note="Toprim"
FT   DOMAIN          1107..1222
FT                   /note="DOD-type homing endonuclease"
FT   ZN_FING         9..30
FT                   /note="C4-type 1"
FT                   /evidence="ECO:0000250"
FT   ZN_FING         723..742
FT                   /note="C4-type 2"
FT                   /evidence="ECO:0000250"
FT   REGION          646..1624
FT                   /note="Topoisomerase I"
FT   MOTIF           213..216
FT                   /note="DEAD box"
FT   ACT_SITE        1366
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         646
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000250"
FT   BINDING         772
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000250"
FT   BINDING         772
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
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"
SQ   SEQUENCE   1624 AA;  187069 MW;  B897F8F42FEB6EF5 CRC64;
     MKAIYRGMCP NCRGAITDER LSNKNPCEGC LSEPILSEDY NELIVAVRNA LKLRGTLKDW
     EELYRLNKEV SEIEELFEKS TGFKFWSAQR TWVKRIIRGK SFSIIAPTGM GKSTFGAFIS
     IYFATKGKKS YIVVPTTPLV IQTVKKIESM LEKANVSVRL VYYHGNLRKK EKEEALEKIR
     NGDFDILITS SQFLATRFKE LLKDKKFDLI FVDDVDAFLK ASKNIDRSLI MLGFSEEIIG
     RAWEVIKLKK QLAKLLQNEK KNEEEIEKLN KEIEKIEDEI EEYKRRNKIG ILIVASATGS
     AKGDRIKLYR ELLGFEVGSG RSVLRNIVDT YLLPEKPIEE HVVELLRKLG KGGLIFVPID
     KGIEYAEELT DYLKSQGFKV ELVSAKNKKG LELFEKGEID YLVGVATYYG TLVRGLDLPH
     LIRFAIFTGV PKFRFSMDLE QPTIYRVLGL MSEILEFLPE EKKSEGEKLY ARLRRLIRNI
     PQYELMKIEE ALAEGLELEG FHNHVLEVFK QSVEFLREVL KDEEVIKKIA ENPFLSLKEI
     EGKLYIEIPD VRTYIQASGR TSRLFAGGIT KGLSVIIVDD QKVFNGLIRQ MRWRFVEFDI
     KKFEEVNLKE VLKEIDRDRE KVKLVIEGKI SEQVKDLVKS ALMIVESPNK ARTIASFFGQ
     PSKRKIGDLT AYEVSIGDKM LTILASGGHM FDLVTNEGYH GVLILKNNGK PYFVPVYDTI
     KRCRDCGHQF VDWEQKGVCP RCGSRNVHDA LENVKAMREL ALEVDEILIG TDPDTEGEKI
     AWDIRNVLAP YAPNIKRIEF HEVTRPAILR AIREARDINE DRVNAQLVRR IEDRWIGFEL
     SQKLWEVFEN RNLSAGRVQT PVLGWIVQRY KEFTESETDF LGIILENGIN VTIENAKGEV
     REVEVKDVII EEKDVNPLPP YTTDTMLQDA SRFLGFSATK TMQLAQDLFE AGLCVTPDTL
     VSLSDGRIIE IREAVENSEE SLLGINGLKP KEAKALKFWE IDWDGPIKVI KLKNGHEIKA
     TPDHGLLVMR DGKIGWVSAK NIREGDYVAF IYNLGHRGGK KYTLPQLLKE LGISEYENSS
     SQELNNREQE MDSKQISIEL DERFWYIFGV ILGKGTLKGD KVVIFQKDVK PVIEEALPFV
     RIFESADHIG FSHLILAEVF RRLGVGEGKL HSLVFGLREE YINAMIAGYF DASGTFLRRA
     VLTSKRGDIL RMLSVYLYQI GIVNNLRRDE HAGVWELIIS DLEKFREKIY PYLRIKKSQF
     DKVYSISKNE GDFLPVASIF RKLKFRDGFK NRILDEEIPR DEVAKVLEYA EDSPEKEFLN
     SLVEARVTWV RVEKIEERHY TGKLYDFTTT TENFISNGIV SHNCTYHRTD SIHVSNTGIE
     VAKEYITQEI GEEYFTPRKW GEEGAHEAIR PTRPIDTGRL IQLIRDGIIT IPKNLTRDHF
     RLYDLIFRRF MASQMKPAKI LYEKAIISTP FKDVEVEGYI DVLYDGWSKI KSLPLRQIPK
     LEKGQRLRVK EVKQWRAPKV SLYTQGDVIA LMKERGIGRP STYAKIVQTL LQRGYVIETK
     GKKKLVPTEK GIKVYQYLIT KYKDLVSEER TRQLEKIMDM VEEAKADYQD VLNELYEEIK
     RYVR