RGYR_METJA
ID RGYR_METJA Reviewed; 1613 AA.
AC Q58907;
DT 16-FEB-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 148.
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=Mja r-Gyr intein;
GN Name=rgy; OrderedLocusNames=MJ1512;
OS Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM
OS 10045 / NBRC 100440) (Methanococcus jannaschii).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanocaldococcaceae; Methanocaldococcus.
OX NCBI_TaxID=243232;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=8688087; DOI=10.1126/science.273.5278.1058;
RA Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G.,
RA Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R.,
RA Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R.,
RA Kirkness E.F., Weinstock K.G., Merrick J.M., Glodek A., Scott J.L.,
RA Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R.,
RA Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D.,
RA Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P.,
RA Fraser C.M., Smith H.O., Woese C.R., Venter J.C.;
RT "Complete genome sequence of the methanogenic archaeon, Methanococcus
RT jannaschii.";
RL Science 273:1058-1073(1996).
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; L77117; AAB99531.1; -; Genomic_DNA.
DR PIR; G64488; G64488.
DR RefSeq; WP_010871035.1; NC_000909.1.
DR AlphaFoldDB; Q58907; -.
DR SMR; Q58907; -.
DR STRING; 243232.MJ_1512; -.
DR PRIDE; Q58907; -.
DR EnsemblBacteria; AAB99531; AAB99531; MJ_1512.
DR GeneID; 1452419; -.
DR KEGG; mja:MJ_1512; -.
DR eggNOG; arCOG01526; Archaea.
DR eggNOG; arCOG03145; Archaea.
DR HOGENOM; CLU_002886_0_0_2; -.
DR InParanoid; Q58907; -.
DR OMA; GVATYYG; -.
DR OrthoDB; 1837at2157; -.
DR PhylomeDB; Q58907; -.
DR Proteomes; UP000000805; 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; 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; IPR001650; Helicase_C.
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; IPR006142; INTEIN.
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; 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; PR00379; INTEIN.
DR PRINTS; PR00417; PRTPISMRASEI.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 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; PS51194; HELICASE_CTER; 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; Topoisomerase; Zinc; Zinc-finger.
FT CHAIN 1..866
FT /note="Reverse gyrase, 1st part"
FT /evidence="ECO:0000255"
FT /id="PRO_0000030353"
FT CHAIN 867..1360
FT /note="Mja r-Gyr intein"
FT /evidence="ECO:0000255"
FT /id="PRO_0000030354"
FT CHAIN 1361..1613
FT /note="Reverse gyrase, 2nd part"
FT /evidence="ECO:0000255"
FT /id="PRO_0000030355"
FT DOMAIN 87..291
FT /note="Helicase ATP-binding"
FT DOMAIN 310..525
FT /note="Helicase C-terminal"
FT DOMAIN 550..712
FT /note="Toprim"
FT DOMAIN 1070..1199
FT /note="DOD-type homing endonuclease"
FT ZN_FING 10..30
FT /note="C4-type"
FT /evidence="ECO:0000250"
FT REGION 556..1613
FT /note="Topoisomerase I"
FT MOTIF 203..206
FT /note="DEAD box"
FT ACT_SITE 1363
FT /note="For DNA cleavage activity"
FT /evidence="ECO:0000250"
FT BINDING 83
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 100..107
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 556
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 681
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 681
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 683
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
SQ SEQUENCE 1613 AA; 188257 MW; 7170C4E120237AE3 CRC64;
MIPMIYKEMC PNCNGEITSE RLAIGVCEKC LKEENVFEKL KLCEKLREEK TLKNLKDYCI
IWNEFKEFEE FVKDLGFELL SIQKMWAKRV LKNKSFSIVV PTGVGKSFFG ILMSLFLAKK
GKRCYIILPT TLLVKQTYEK ISSLTEKNNL NIRVVAYHSE LSTKEKKEVK ERIENNDYDV
LITTSNYLTK NMPKCKFDFV FVDDVDALLK ASKNIDRTLK LLGFDEEIIN EAYKIIYLIK
IGKIEDAMKK REILKKKISK IKHGCLIIAS ATGKSYGDRV KLYRELLDFE IGFGMNKLRD
VVDIYDEEFS KEKILEYIKL FGSGGIVFVS IDYGVEKAQE IEKYLLENNI KAKLIHSKDK
KGFDDFREGK IDVLIGVASY YGVLVRGLDM PERVRYAIFY GIPKFKIRLK EYINSLKEKG
ELKEDINIEG KTEEEIRQII TEKLKIKNFS LRKEDDEYLL LIPDVKTYIQ ASGRTSRMTE
FGLTKGASIV LVDEKEIFEA LKKYMLFMYE SEFKRIDEVN LEELIKKIDE DREKIKVGRA
KGKVPDLLKS VLMVVESPNK ARTIANFFGK PSVRKINNRN VYEVCIGDLN LIITASGGHV
FDLVTKEGFY GVKIENNLYI PIYTSIKKVN GEQFTDQKDL EELIKQLMEK GERVNAMDAK
ENIEIIREIA DEVDAIFIAT DIDTEGEKIG YDIAINALPF NRNIYRVGFN EITKRAILKA
VESFKKGEEL SLDENKVKGQ VVRRIEDRWI GFRLSQKLWE VFNKNYLSAG RVQTPVLGWI
IERYNEHKIK VPYLSLKLEN DIYIGKIWED EFDKDEVEVE VKVYEKEIPP LPPFTTDTLL
EEATKRFGLS TDEIMSIAQE LFELGLCLTP DTYVVLGDGR IETIEDIVNA KERNVLSLDL
DNLSIKIDTA IKFWKLRYNG NLSKITLSNN YELKATPDHC LLVLRDNQLK WIPAKDIKEN
DYIAMPFNYK VERKPISLLN LLKYLDITDV LIEFDENSTI FEKIAEYIRN NIKTSTKYKY
LRNRRVPLKY LIEWNFDLDE IEKEAKYIYK SVAGTKKIPL FKLDERFWYF AGLVLGDGSI
QDSKIRIAQT PLKDVKSILD ETFPFLHNWI SGNQVIISNP IIAEILEKLG MRNGKLNGII
FSLPESYINA LIAGYFDTDG CFSLLYDKKA KKHNLRMVLT SKRRDVLEKI GIYLNSIGIL
NTLHKSREVY SLIISNKSLE TFKEKIAKYL KIRKEAFING YKTYKKEHEE RFECDLLPVK
EVFKKLTFEK GRKEILKDSK IHIENWYKEK TNNIPREKLK TVLRYANNSE HKEFLEKIVN
GDISFVRVKK VENIPYDGYV YDLSIKHNQN FISNGVISHN CTYHRTSSTR VSLDGMRVAR
EYLKLNNLED YLKNREYFME GAHECIRPTK PMNTDELIEF LKENNIKLTK NHIKVYDLIF
RRFIASQMKE AVVEYEEIYI KDLDEKVEGY VDIKFDGWSR IYNLKLKKLP RIEKSSLKVL
DKKLRKIPKV PLYDEGEVVK LMKERGIGRP STYAQIIKKL LDRGYVVKSK DKNKLIPTKL
GIEVYNYLIN NYPHLISEER TRELEEIMDK IENGEVDYIE VLKALHEEIL SIR
