ID B7R1X7_9EURY Unreviewed; 1714 AA.
AC B7R1X7;
DT 10-FEB-2009, integrated into UniProtKB/TrEMBL.
DT 10-FEB-2009, sequence version 1.
DT 27-MAR-2024, entry version 95.
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 ORFNames=TAM4_1673 {ECO:0000313|EMBL:EEB74306.1};
OS Thermococcus sp. AM4.
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Thermococcus.
OX NCBI_TaxID=246969 {ECO:0000313|EMBL:EEB74306.1, ECO:0000313|Proteomes:UP000009277};
RN [1] {ECO:0000313|EMBL:EEB74306.1, ECO:0000313|Proteomes:UP000009277}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AM4 {ECO:0000313|EMBL:EEB74306.1,
RC ECO:0000313|Proteomes:UP000009277};
RX PubMed=22123768; DOI=10.1128/JB.06259-11;
RA Oger P., Sokolova T.G., Kozhevnikova D.A., Chernyh N.A., Bartlett D.H.,
RA Bonch-Osmolovskaya E.A., Lebedinsky A.V.;
RT "Complete Genome Sequence of the Hyperthermophilic Archaeon Thermococcus
RT sp. Strain AM4, Capable of Organotrophic Growth and Growth at the Expense
RT of Hydrogenogenic or Sulfidogenic Oxidation of Carbon Monoxide.";
RL J. Bacteriol. 193:7019-7020(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; CP002952; EEB74306.1; -; Genomic_DNA.
DR RefSeq; WP_014122201.1; NC_016051.1.
DR STRING; 246969.TAM4_1673; -.
DR GeneID; 7420281; -.
DR KEGG; tha:TAM4_1673; -.
DR eggNOG; arCOG01526; Archaea.
DR eggNOG; arCOG03151; Archaea.
DR HOGENOM; CLU_002886_0_0_2; -.
DR OrthoDB; 30963at2157; -.
DR Proteomes; UP000009277; 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: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; 1.
DR CDD; cd18798; SF2_C_reverse_gyrase; 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; 2.
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; 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; 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; 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; 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; PS50880; TOPRIM; 1.
PE 3: Inferred from homology;
KW ATP-binding {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|HAMAP-
KW Rule:MF_01125}; Autocatalytic cleavage {ECO:0000256|ARBA:ARBA00022813};
KW Coiled coil {ECO:0000256|SAM:Coils};
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|ARBA:ARBA00022741, ECO:0000256|HAMAP-
KW Rule:MF_01125}; Protein splicing {ECO:0000256|ARBA:ARBA00023000};
KW Repeat {ECO:0000256|ARBA:ARBA00022737};
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 93..256
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000259|PROSITE:PS51192"
FT DOMAIN 642..805
FT /note="Toprim"
FT /evidence="ECO:0000259|PROSITE:PS50880"
FT DOMAIN 1160..1287
FT /note="DOD-type homing endonuclease"
FT /evidence="ECO:0000259|PROSITE:PS50819"
FT DOMAIN 1428..1449
FT /note="Intein C-terminal splicing"
FT /evidence="ECO:0000259|PROSITE:PS50818"
FT REGION 638..1714
FT /note="Topoisomerase I"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01125"
FT COILED 260..287
FT /evidence="ECO:0000256|SAM:Coils"
FT ACT_SITE 1451
FT /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01125"
FT BINDING 89
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01125"
SQ SEQUENCE 1714 AA; 197397 MW; 7FB98F1EF0BBBAE4 CRC64;
MKALYREMCP NCRGRISDER LSMRNPCESC LNEPIAIDSY FELVSAVRDA LLNASRLKDW
ERIYRLESET REIEDFFRKA TGFTFWSAQR TWVKRLLKGR SFSIIAPTGM GKSTFGAFMS
VYYATKGKKS YIVVPTTPLV IQTIRKVQAI IERTGLNVNL AYYHGNLRKK EKEEMLAKIE
SGDYDILITS AQWLARNFDE KLKGRHFDFI FVDDVDAFLK ASKNIDRSLL LLGFTEEIIG
KAWEIIRLKK QMARYLNGNS QDKNDRLKEL NEAIEKIQRE IEEFKRKNDI GIMIIASATG
SARGDRIKLY RELLGFEVGS GRSALRNVVD SYLKPSKDVK EHVEELLRKL GKGGLIFVPI
DQGLSYAEEL VDYLKERGFA VELASSKNKK AVERFENGEA DYLVGVATYY GSIVRGLDLP
HLIRYAVFTG VPKFRFSIDL ERPTIYRALG LLSEVMDFLD DEDRRKAEKL HARLRRLIRN
IPQFELLKIE EALAEGLPIE NDFHKTVLNV FRELVEFLRE VLKKEDVLKR LAEDPFVSLV
KEEGKWFIEI PDVRTYIQAT GRTSRLFAGG ITKGLSVLIV DNEKVFNGLV RQMRWRFTEF
KMVPFEELDL EKLLKEIDED REKVKLVMEG KISSKVKDLV KSALMIVESP NKARTIANFF
GRPSKTRIGE LVAYEVSVGD KMLTILASGG HMFDLVTNEG YHGVLIEREG DMLKFIPVYD
TIKRCRDCGY QFVDWEERGV CPRCGSRNVH DALENVKAMR EIAQEVDEIL IATDPDTEGE
KIAWDIRNVL APYTPNIKRV EFHEVTRPAI MKAIREARDV NEARVEAQMV RRIEDRWIGF
ELSQELQRVF ENRNLSAGRV QTPVLGWIIE RYKEFTESEV YFLGLTLENG LQVTVELGKD
GKDVEPPEYV TVEEVQLEER ELNPAPPYTT DAMLRDASTF LKLSAPETMR LAQDLFEAGL
CVTPDTVVTL ADGRIMRIKD AVRSKEGNLL AVNGLKAKNA KATKFWEINW NGPLKVVRLQ
NGHEIRATPD HGLLVLRDGK LGWVSTKNIE PGDYVAFAYN TGHKGTREYT LLEMLIELGI
TDVMVELKGE YFDSKIAPLV RERIKTSTKY KYLRNRVVPL AKLVEWGVDD YEPHVVSIYR
QRAGSRRIPN FKLDENFWYV FGLVLGDGTL RGSKVLISQT PLKQVKEILE ETFPFLHVFE
TTNQVGFSNS ILVELFRRLG GRSGELNPII FTIPEKMLNA MIAGYFDTDG TFSLLHDKRG
VNFRALLTSK RGDVLKKLSV YLYQVGILNY LKRDKRTGVW DLIISNRSLG IFREKIYPYL
RIRRAQFEET YSAYRRTRKP NESDTIPIGA LIKELIFPNG TKARLLREEG IDIWNWLKKP
GSVPRNKLAK VLEYVEDNEV KDYLRSLVEA NVTWVKVVDV DEEHYTGKLY DFTTTTENFI
ANGAVSHNCT YHRTDSTHVS STGIEIAKEY ITSELGEEYF KPRPWGEEGT HEAIRPTRPI
DTGRLMQLIR DGVIQLPRNL TRNHYRLYDM IFRRFMTSQM VPAVILHERA VINAGVGKVE
LEGYVEILKD GWTKLRSPPL RQLPKLEPGA KLKVVEFKKW KAPKVSLYTQ GDIIALMKER
GIGRPSTYAK IVQTLLQRYY VFETRGRKKL VPTEKGIKVY HYLISKYREL VSEEKTRELE
EKMDLIEEGK LNYLEVLNEL YREIACEIRK EGCS
//
