ID D3RWU3_FERPA Unreviewed; 1072 AA.
AC D3RWU3;
DT 20-APR-2010, integrated into UniProtKB/TrEMBL.
DT 20-APR-2010, sequence version 1.
DT 27-MAR-2024, entry version 94.
DE RecName: Full=Reverse gyrase {ECO:0000256|HAMAP-Rule:MF_01125, ECO:0000256|RuleBase:RU004026};
DE EC=5.6.2.- {ECO:0000256|HAMAP-Rule:MF_01125};
GN Name=rgy {ECO:0000256|HAMAP-Rule:MF_01125};
GN OrderedLocusNames=Ferp_0787 {ECO:0000313|EMBL:ADC64956.1};
OS Ferroglobus placidus (strain DSM 10642 / AEDII12DO).
OC Archaea; Euryarchaeota; Archaeoglobi; Archaeoglobales; Archaeoglobaceae;
OC Ferroglobus.
OX NCBI_TaxID=589924 {ECO:0000313|EMBL:ADC64956.1, ECO:0000313|Proteomes:UP000002613};
RN [1] {ECO:0000313|Proteomes:UP000002613}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 10642 / AEDII12DO {ECO:0000313|Proteomes:UP000002613};
RG US DOE Joint Genome Institute;
RA Lucas S., Copeland A., Lapidus A., Cheng J.-F., Bruce D., Goodwin L.,
RA Pitluck S., Saunders E., Brettin T., Detter J.C., Han C., Tapia R.,
RA Larimer F., Land M., Hauser L., Kyrpides N., Ivanova N., Holmes D.,
RA Lovley D., Kyrpides N., Anderson I.J., Woyke T.;
RT "Complete sequence of Ferroglobus placidus DSM 10642.";
RL Submitted (FEB-2010) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:ADC64956.1, ECO:0000313|Proteomes:UP000002613}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 10642 / AEDII12DO {ECO:0000313|Proteomes:UP000002613};
RX PubMed=22180810; DOI=10.4056/sigs.2225018;
RA Anderson I., Risso C., Holmes D., Lucas S., Copeland A., Lapidus A.,
RA Cheng J.F., Bruce D., Goodwin L., Pitluck S., Saunders E., Brettin T.,
RA Detter J.C., Han C., Tapia R., Larimer F., Land M., Hauser L., Woyke T.,
RA Lovley D., Kyrpides N., Ivanova N.;
RT "Complete genome sequence of Ferroglobus placidus AEDII12DO.";
RL Stand. Genomic Sci. 5:50-60(2011).
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. Involved in rewinding DNA strands in regions of
CC the chromosome that have opened up to allow replication, transcription,
CC DNA repair and/or for DNA protection. {ECO:0000256|RuleBase:RU004026}.
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:0000256|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;
CC Evidence={ECO:0000256|ARBA:ARBA00001836, ECO:0000256|HAMAP-
CC Rule:MF_01125, ECO:0000256|RuleBase:RU004026};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|ARBA:ARBA00001946};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01125};
CC Note=Binds 1 or 2 zinc ions per subunit. {ECO:0000256|HAMAP-
CC Rule:MF_01125};
CC -!- SUBUNIT: Monomer. {ECO:0000256|HAMAP-Rule:MF_01125}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|ARBA:ARBA00004496,
CC ECO:0000256|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:0000256|HAMAP-Rule:MF_01125}.
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:0000256|HAMAP-
CC Rule:MF_01125}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the type IA
CC topoisomerase family. {ECO:0000256|HAMAP-Rule:MF_01125}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the DEAD box helicase
CC family. DDVD subfamily. {ECO:0000256|ARBA:ARBA00043976,
CC ECO:0000256|HAMAP-Rule:MF_01125}.
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DR EMBL; CP001899; ADC64956.1; -; Genomic_DNA.
DR RefSeq; WP_012965299.1; NC_013849.1.
DR AlphaFoldDB; D3RWU3; -.
DR STRING; 589924.Ferp_0787; -.
DR PaxDb; 589924-Ferp_0787; -.
DR GeneID; 8778293; -.
DR KEGG; fpl:Ferp_0787; -.
DR eggNOG; arCOG01526; Archaea.
DR HOGENOM; CLU_002886_0_0_2; -.
DR OrthoDB; 30963at2157; -.
DR Proteomes; UP000002613; 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:0003918; F:DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity; IEA:UniProtKB-UniRule.
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 CDD; cd17924; DDXDc_reverse_gyrase; 1.
DR CDD; cd18798; SF2_C_reverse_gyrase; 1.
DR CDD; cd00186; TOP1Ac; 1.
DR CDD; cd03361; TOPRIM_TopoIA_RevGyr; 1.
DR Gene3D; 2.60.510.20; -; 1.
DR Gene3D; 3.30.56.120; -; 1.
DR Gene3D; 3.40.1360.10; -; 1.
DR Gene3D; 3.40.50.140; -; 1.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 2.
DR Gene3D; 2.20.20.30; reverse gyrase domain; 1.
DR Gene3D; 1.10.460.10; Topoisomerase I, domain 2; 1.
DR Gene3D; 1.10.290.10; Topoisomerase I, domain 4; 1.
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 NCBIfam; TIGR01054; rgy; 1.
DR PANTHER; PTHR43505; REVERSE GYRASE; 1.
DR PANTHER; PTHR43505:SF1; REVERSE GYRASE; 1.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF01131; Topoisom_bac; 2.
DR Pfam; PF01751; Toprim; 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; P-loop containing nucleoside triphosphate hydrolases; 2.
DR SUPFAM; SSF56712; Prokaryotic type I DNA topoisomerase; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS50880; TOPRIM; 1.
PE 3: Inferred from homology;
KW ATP-binding {ECO:0000256|HAMAP-Rule:MF_01125,
KW ECO:0000256|RuleBase:RU004026};
KW Cytoplasm {ECO:0000256|ARBA:ARBA00022490, ECO:0000256|HAMAP-Rule:MF_01125};
KW DNA-binding {ECO:0000256|ARBA:ARBA00023125, ECO:0000256|HAMAP-
KW Rule:MF_01125}; Hydrolase {ECO:0000256|HAMAP-Rule:MF_01125};
KW Isomerase {ECO:0000256|ARBA:ARBA00023235, ECO:0000256|HAMAP-Rule:MF_01125};
KW Metal-binding {ECO:0000256|HAMAP-Rule:MF_01125,
KW ECO:0000256|RuleBase:RU004026};
KW Nucleotide-binding {ECO:0000256|HAMAP-Rule:MF_01125,
KW ECO:0000256|RuleBase:RU004026};
KW Reference proteome {ECO:0000313|Proteomes:UP000002613};
KW Topoisomerase {ECO:0000256|ARBA:ARBA00023029, ECO:0000256|HAMAP-
KW Rule:MF_01125};
KW Zinc {ECO:0000256|ARBA:ARBA00022833, ECO:0000256|HAMAP-Rule:MF_01125};
KW Zinc-finger {ECO:0000256|ARBA:ARBA00022771, ECO:0000256|HAMAP-
KW Rule:MF_01125}.
FT DOMAIN 65..251
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000259|PROSITE:PS51192"
FT DOMAIN 519..680
FT /note="Toprim"
FT /evidence="ECO:0000259|PROSITE:PS50880"
FT REGION 515..1072
FT /note="Topoisomerase I"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01125"
FT ACT_SITE 828
FT /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01125"
FT BINDING 61
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01125"
SQ SEQUENCE 1072 AA; 123936 MW; 1A891DE643C43449 CRC64;
MIPVKYANLC SVCHKDVTWE ELEKSYCRFK KLPQCSSFLD KIYKEFEEFF KKIIGEPRSI
QKFWAKRVLS FESFAAVAPT GIGKTSFGSA MALFLALKKR KSYIILPTTL LVAQVVENLK
KYCEKAGIDC GLNEEKEVTI AYYHGKLKEK DKFFEILEKN SFDILVTTTQ FLPRYFEKLN
GKIFNFIFVD DVDAVLKASR NVDRILKLLG FRYKNGKWEG KPKGVLMVST ATAKKGQKVK
LFRELLNFDV GTSTHAVRNI DDVYVERADV EAVKEILRKM GSGGLIYARS SEEAEELYNS
LKDEFKVGLV TAQRKKDFVL FERGEIDYLI GTAYYYGTLV RGLDLPERIR FAVFFKAPVF
RVRIEDIDTI SPGMVRVIAL IFKEDERVKK FIPYLPKITE GTKEFEELKS ILKKVIAERK
KEVKDFVLRE GEVIFPDVRT YIQGSGRTSR LFAGGITKGA SFLLEDDEDV LKAFVERARY
FDIEFKKIDE VDFESLIREI NESREKFRRR AEFKDVIKPT LFIVESPTKA RQISRFFGQP
SVKVIGDEND VHVVAYEVPT PERILIVTAS LGHVTDLITN RAFHGVEVNG IFVPIYASIK
RCRDCGYQFT EERENCPKCE SSNIDDSKKR IEALRRLAKE TGEVIIGTDP DSEGEKIAWD
IKNLLSGCAT IKRAEFHEVT RRAVTEALAN LRDVDENLVK AQIVRRVEDR WIGFILSQKL
WEVFKNRNLS AGRAQTPVLG WIIQRAEENK KKKTVAFVKE LGLSLEGIAK KELELEIELI
EKKEEERTPL PPYTTDSMLR DANAILKMSA KDAMQIAQEL FEHGLITYHR TDSTRVSEVG
LRIAKEYLGE YFTPREWFAE GAHECIRPTR AIDRDTLQRL ISEGIIVVEN FTWRHFALYD
LIFRRFMASQ CKPYKVVVAK YRIKADGKEF EEERIIKAEG RAYELYKSVW VRNELPTGKI
KVEAEIRRVP AAPLYTQSDV VALMKERRIG RPSTYATIVD KLFQRNYIIE KGGKLVPTKL
GYSVYEYLIN NYRSFVSEER TRLLEEMMDK VERGEADYFE TLKEMYNEVK QI
//
