RGYR_PYRFU
ID RGYR_PYRFU Reviewed; 1214 AA.
AC P95479; Q8U3H2;
DT 16-FEB-2004, integrated into UniProtKB/Swiss-Prot.
DT 16-FEB-2004, sequence version 2.
DT 03-AUG-2022, entry version 139.
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}; OrderedLocusNames=PF0495;
OS Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=186497;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=9045834; DOI=10.1128/jb.179.5.1721-1726.1997;
RA Borges K.M., Bergerat A., Bogert A.M., DiRuggiero J., Forterre P.,
RA Robb F.T.;
RT "Characterization of the reverse gyrase from the hyperthermophilic archaeon
RT Pyrococcus furiosus.";
RL J. Bacteriol. 179:1721-1726(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=10430560; DOI=10.1093/genetics/152.4.1299;
RA Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M.,
RA DiRuggiero J., Robb F.T.;
RT "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P.
RT horikoshii inferred from complete genomic sequences.";
RL Genetics 152:1299-1305(1999).
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.
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.
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}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; U66557; AAB49283.1; -; Genomic_DNA.
DR EMBL; AE009950; AAL80619.1; -; Genomic_DNA.
DR RefSeq; WP_011011612.1; NZ_CP023154.1.
DR AlphaFoldDB; P95479; -.
DR SMR; P95479; -.
DR IntAct; P95479; 1.
DR STRING; 186497.PF0495; -.
DR PRIDE; P95479; -.
DR EnsemblBacteria; AAL80619; AAL80619; PF0495.
DR GeneID; 41712297; -.
DR KEGG; pfu:PF0495; -.
DR PATRIC; fig|186497.12.peg.518; -.
DR eggNOG; arCOG01526; Archaea.
DR HOGENOM; CLU_002886_0_0_2; -.
DR OMA; GVATYYG; -.
DR OrthoDB; 1837at2157; -.
DR PhylomeDB; P95479; -.
DR BRENDA; 3.6.4.12; 5243.
DR BRENDA; 5.6.2.2; 5243.
DR Proteomes; UP000001013; 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; 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; 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; Reference proteome; Repeat;
KW Topoisomerase; Zinc; Zinc-finger.
FT CHAIN 1..1214
FT /note="Reverse gyrase"
FT /id="PRO_0000158089"
FT DOMAIN 93..252
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"
FT CONFLICT 280
FT /note="E -> D (in Ref. 1; AAB49283)"
FT /evidence="ECO:0000305"
FT CONFLICT 937
FT /note="A -> P (in Ref. 1; AAB49283)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1214 AA; 139984 MW; 7B854F084C254EE6 CRC64;
MKAIYRDMCP NCRGAITDER LAAKNPCDAC LDEPISMDDY FQLVTAIRKA LKLKGVLKEW
EEIYALNKEV KEIEELFKKA TGFTFWSAQR SWVKRIIKGK SFSIIAPTGM GKSTFGAFMS
IYFALKGKKS YIVVPTTPLV VQTVKKIKAM MEKAEVKVNL VYYHGNLKKK EKDEALEKIK
SGNFDILVTS SQFLATRFDE LLKDKRIDFM FVDDVDAFLK ASKNIDRSLM MLGFNEEIIK
KAWEIIKLKK QLAKLLQNES GNEEVEKLNR EIERLEREIE RYKKENKIGI LIVASATGSA
RGDRIKLYRE LLGFEVGSGR SVLRNIVDTY IIPEKSMEEH VEELLKTLGR GGLIFVPIDK
GIEYAEQLTN YLKSKGFKVE LVSARDKKGL ELFEKEEVDY LVGVATYYGT IVRGLDLPHL
VRFAIFTGVP KFRFSLDLEQ PTIYRVLGLM SEILEFLPEE KRTEGEKLYA RLRRLIRNIP
QYELMKIEEA LAEGLELEGF YNHVLEVFKQ AVEFLREALK DEEVLKKIAE NPFLSLKQIE
GKWYIEIPDV RTYIQASGRT SRLFAGGITK GLSVILVDDQ KVFNGLIRQM RWRFVEFEIK
PLGEINIEEV LKEIDRDREK VRLVLEGKIS EQVKDLVKSA LMIVESPNKA RTIANFFGQP
SKRRIGDLVA YEVSIGDKML TILASGGHMF DLVTTEGYHG VLLLEKGGKR YFVPVYDTIK
RCRDCGHQFV DWEEKGVCPR CGSRNVYDAL ENVKAMRDLA QEVDEILIGT DPDTEGEKIA
WDIRNVLSPY APVIKRIEFH EVTRPAILRA INEARDINED RVNAQLVRRI EDRWIGFELS
QKLWEVFENY NLSAGRVQTP VLGWIVQRYK EFTESETDFL GLTLENDITI ILEGVSGDVQ
EVYVKEVTIE EREINPLPPY TTDAMLQDAS RFLGFSATHT MQLAQDLFEL GLTTYHRTDS
IHVSNTGIEI AKEYITQEIG EEYFAPRKWG EEGAHEAIRP TRPIDTGRLI QLIRDGIITL
PRNLTKDHFK LYDLIFRRFM ASQMKPAKVL YERAVIGTPY GEVEIEGYID VIYDGWSRIK
PLPLKKLPRL EKDQILKVTE IRKWRAPKVS LYTQGDVIAL MKERGIGRPS TYAKIVQTLL
QRGYVIETKS KKKLVPTEKG IKVYHYLVSK YKDLVSEERT RQLEKLMDMV EEAKANYQEV
LNELYEEILR YVKS
