ID F6BC58_METIK Unreviewed; 1119 AA.
AC F6BC58;
DT 27-JUL-2011, integrated into UniProtKB/TrEMBL.
DT 27-JUL-2011, sequence version 1.
DT 27-MAR-2024, entry version 82.
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=Metig_0585 {ECO:0000313|EMBL:AEF96139.1};
OS Methanotorris igneus (strain DSM 5666 / JCM 11834 / Kol 5).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanocaldococcaceae; Methanotorris.
OX NCBI_TaxID=880724 {ECO:0000313|Proteomes:UP000009227};
RN [1] {ECO:0000313|EMBL:AEF96139.1, ECO:0000313|Proteomes:UP000009227}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 5666 / JCM 11834 / Kol 5
RC {ECO:0000313|Proteomes:UP000009227};
RG US DOE Joint Genome Institute;
RA Lucas S., Han J., Lapidus A., Cheng J.-F., Goodwin L., Pitluck S.,
RA Peters L., Mikhailova N., Chertkov O., Han C., Tapia R., Land M.,
RA Hauser L., Kyrpides N., Ivanova N., Pagani I., Sieprawska-Lupa M.,
RA Whitman W., Woyke T.;
RT "Complete sequence of Methanotorris igneus Kol 5.";
RL Submitted (MAY-2011) to the EMBL/GenBank/DDBJ databases.
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; CP002737; AEF96139.1; -; Genomic_DNA.
DR RefSeq; WP_013798746.1; NC_015562.1.
DR AlphaFoldDB; F6BC58; -.
DR STRING; 880724.Metig_0585; -.
DR GeneID; 10643423; -.
DR KEGG; mig:Metig_0585; -.
DR HOGENOM; CLU_002886_0_0_2; -.
DR OrthoDB; 30963at2157; -.
DR Proteomes; UP000009227; 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; 3.40.50.140; -; 1.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 3.
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; IPR001650; Helicase_C.
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; TIGR01054; rgy; 2.
DR PANTHER; PTHR43505; REVERSE GYRASE; 1.
DR PANTHER; PTHR43505:SF1; REVERSE GYRASE; 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; SM00490; HELICc; 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|ARBA:ARBA00022840, ECO:0000256|HAMAP-
KW Rule:MF_01125};
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}; Reference proteome {ECO:0000313|Proteomes:UP000009227};
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 85..244
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000259|PROSITE:PS51192"
FT DOMAIN 542..705
FT /note="Toprim"
FT /evidence="ECO:0000259|PROSITE:PS50880"
FT REGION 538..1119
FT /note="Topoisomerase I"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01125"
FT ACT_SITE 869
FT /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01125"
FT BINDING 81
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01125"
SQ SEQUENCE 1119 AA; 129905 MW; 13B97930CBE65549 CRC64;
MVPIIFKNMC PNCHSDIESL RLDKGLTCKN CMEDDSVSNI CKYLAEKNTL KALEDYCKLK
NELKELEDVA ERCGFKLLSI QRMWAKRVLK NKSFSIVAPT GVGKSVFGMI TAIYFATKNK
KSYIILPTTL LVKQTYEKII NMANKAGVEV NVVAYHSELS SEEKRVAKEK IEKKDYNILI
TTSNYLSKNP IDDKFDFVFI DDVDAFLKAS KNIDKSLKLL GFSDEIIKKA YNILYLIRKK
KIEDALKERE KLKEMISKIN HGCMIVASAT GKSYGDKVKL YRELLDFEIG YGMSKLRDVE
DIYDENLSME KILEYIKIFG DGGIIFVPID YGLKKAEEIE EFLIKNGIKA KLIHSKDKKG
FEEFKNGEID VLIGVASYYG VLVRGLDIPE RIRYCIFYGV PKFKIDLEET LKKENENISI
EGLNEEELME LVKNTLKIKN FSLRKEDNKY YLLIPDVKTY IQTSGRTSRM TENGLIKGAS
IVLVDDAEVF EGLKKYMLFM YEGEFKRIDE IDVEKLIEKI DEDRRKLKET KEKNKVPDLL
KSALMVVESP NKARTIANFF GKPSVRRINN KKVYEVCIGD WNLIITASGG HIFDLVTKEG
YHGVLIGNNS YIPIYGTIKR VNGEQFVDEK NIEELIKRIK EKTNENIVIH DAKENIEILR
DLASEVDAVF IATDIDVEGE KIGYDIYLNL KPFNKNIFRI GFNEITKRAI MNAIKIVKEG
KSEELSLDEN KVRAQVVRRI EDRWIGFELS KKLWDAFNNT YLSAGRVQTP VLGWIIDRYN
EYQIKVPYLY LKLEDDISFG TIVDDETAKK IKDKDYVDVE VNVYEKDIYP NPPFTTDTLL
EEATKRFGLS SDEVMKIAQE LFELGLTTYH RTSSTRVSLD GMRVAREYLE FNDMLDYLKN
REYYMEGAHE CIRPTKPMDT SELIEFIKNN NIYLTKDHIK IYDLIFRRFI ASQMKECKVE
YEEITIKDLD TKVEGYTNII YDGWTKIYNL KLRKLPKIEK NTLKIIEKSI RKVPKVSLYD
EGEIIKLMKE RGIGRPSTYA QIVKKLFDRK YVLKSKDKGK IIPTKLGIEV YNYLKNNYYN
LICEERTREL ENVMDKIEKG EVEYIKVLDE LLNEIKSIT
//
