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 27-MAR-2024, entry version 146.
DE RecName: Full=Reverse gyrase {ECO:0000255|HAMAP-Rule:MF_01125};
DE EC=5.6.2.- {ECO:0000255|HAMAP-Rule:MF_01125};
DE Contains:
DE RecName: Full=Pho r-Gyr intein;
GN Name=rgy {ECO:0000255|HAMAP-Rule:MF_01125}; 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, increasing the linking number
CC in steps of +1. Binds to single-stranded DNA, transiently cleaves and
CC then rejoins the ends, introducing a positive supercoil in the process.
CC The scissile phosphodiester is attacked by the catalytic tyrosine of
CC the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-
CC enzyme intermediate. Probably involved in rewinding DNA strands in
CC regions of the chromosome that have opened up to allow replication,
CC transcription, DNA repair and/or for DNA protection.
CC {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; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01125};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01125};
CC Note=Binds 2 zinc ions per subunit. {ECO:0000255|HAMAP-Rule:MF_01125};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01125};
CC -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_01125}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01125}.
CC -!- DOMAIN: Introduction of positive supercoils requires the cooperation of
CC both domains. The helicase-like domain probably does not directly
CC unwind DNA, but more likely acts by driving ATP-dependent
CC conformational changes within the whole enzyme. A beta hairpin in the
CC 'latch' region of the N-terminal domain plays a regulatory role in the
CC enzyme, repressing topoisomerase activity in the absence of ATP and
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 -!- 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 known and seems to be essential for
CC adaptation to life at high temperatures. It may play a role in
CC stabilization of DNA at high temperatures. {ECO:0000255|HAMAP-
CC Rule:MF_01125}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the DEAD box helicase
CC family. DDVD subfamily. {ECO:0000255|HAMAP-Rule:MF_01125, ECO:0000305}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the type IA
CC topoisomerase family. {ECO:0000255|HAMAP-Rule:MF_01125}.
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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.gene:9377750; -.
DR EnsemblBacteria; BAA29893; BAA29893; BAA29893.
DR GeneID; 1443130; -.
DR KEGG; pho:PH0800; -.
DR eggNOG; arCOG01526; Archaea.
DR eggNOG; arCOG03151; Archaea.
DR OrthoDB; 30963at2157; -.
DR Proteomes; UP000000752; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:InterPro.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
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:0004386; F:helicase 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 GO; GO:0016539; P:intein-mediated protein splicing; IEA:InterPro.
DR CDD; cd17924; DDXDc_reverse_gyrase; 1.
DR CDD; cd00081; Hint; 2.
DR CDD; cd18798; SF2_C_reverse_gyrase; 1.
DR CDD; cd00186; TOP1Ac; 1.
DR CDD; cd03361; TOPRIM_TopoIA_RevGyr; 1.
DR Gene3D; 3.40.50.140; -; 1.
DR Gene3D; 2.170.16.10; Hedgehog/Intein (Hint) domain; 1.
DR Gene3D; 3.10.28.10; Homing endonucleases; 1.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 3.
DR Gene3D; 1.10.460.10; Topoisomerase I, domain 2; 2.
DR Gene3D; 2.70.20.10; Topoisomerase I, domain 3; 1.
DR Gene3D; 1.10.290.10; Topoisomerase I, domain 4; 1.
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 NCBIfam; TIGR01443; intein_Cterm; 1.
DR NCBIfam; TIGR01445; intein_Nterm; 1.
DR NCBIfam; TIGR01054; rgy; 1.
DR PANTHER; PTHR43505; REVERSE GYRASE; 1.
DR PANTHER; PTHR43505:SF1; REVERSE GYRASE; 1.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF14890; Intein_splicing; 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; Hedgehog/intein (Hint) domain; 1.
DR SUPFAM; SSF55608; Homing endonucleases; 1.
DR SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 2.
DR SUPFAM; SSF56712; Prokaryotic type I DNA topoisomerase; 2.
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; PS52039; TOPO_IA_2; 1.
DR PROSITE; PS50880; TOPRIM; 1.
DR PROSITE; PS52037; ZF_RG_C; 1.
DR PROSITE; PS52036; ZF_RG_N; 1.
PE 3: Inferred from homology;
KW ATP-binding; Autocatalytic cleavage; Cytoplasm; DNA-binding; Isomerase;
KW Magnesium; Metal-binding; Nucleotide-binding; Protein splicing; Repeat;
KW Topoisomerase; Zinc; Zinc-finger.
FT CHAIN 1..1624
FT /note="Reverse gyrase"
FT /id="PRO_0000459348"
FT CHAIN 1..953
FT /note="Reverse gyrase, 1st part"
FT /id="PRO_0000030356"
FT CHAIN 954..1363
FT /note="Pho r-Gyr intein"
FT /id="PRO_0000030357"
FT CHAIN 1364..1624
FT /note="Reverse gyrase, 2nd part"
FT /id="PRO_0000030358"
FT DOMAIN 93..256
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT DOMAIN 640..803
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT DOMAIN 819..1623
FT /note="Topo IA-type catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01383"
FT DOMAIN 1107..1222
FT /note="DOD-type homing endonuclease"
FT ZN_FING 1..42
FT /note="RG N-terminal-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01380"
FT ZN_FING 720..749
FT /note="RG C-terminal-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01381"
FT REGION 636..1624
FT /note="Topoisomerase I"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT MOTIF 213..216
FT /note="DEAD box"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT ACT_SITE 1366
FT /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01383"
FT BINDING 9
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 12
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 27
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 30
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
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 646
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 723
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 726
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 739
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 742
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 772
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
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
//
