ID A0A0F7FJ55_9CREN Unreviewed; 1255 AA.
AC A0A0F7FJ55;
DT 22-JUL-2015, integrated into UniProtKB/TrEMBL.
DT 22-JUL-2015, sequence version 1.
DT 27-MAR-2024, entry version 50.
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=MA03_07680 {ECO:0000313|EMBL:AKG39437.1};
OS Infirmifilum uzonense.
OC Archaea; Thermoproteota; Thermoprotei; Thermofilales; Thermofilaceae;
OC Infirmifilum.
OX NCBI_TaxID=1550241 {ECO:0000313|EMBL:AKG39437.1, ECO:0000313|Proteomes:UP000067434};
RN [1] {ECO:0000313|EMBL:AKG39437.1, ECO:0000313|Proteomes:UP000067434}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=1807-2 {ECO:0000313|EMBL:AKG39437.1,
RC ECO:0000313|Proteomes:UP000067434};
RX PubMed=26664700; DOI=10.1186/s40793-015-0105-y;
RA Toshchakov S.V., Korzhenkov A.A., Samarov N.I., Mazunin I.O., Mozhey O.I.,
RA Shmyr I.S., Derbikova K.S., Taranov E.A., Dominova I.N.,
RA Bonch-Osmolovskaya E.A., Patrushev M.V., Podosokorskaya O.A.,
RA Kublanov I.V.;
RT "Complete genome sequence of and proposal of Thermofilum uzonense sp. nov.
RT a novel hyperthermophilic crenarchaeon and emended description of the genus
RT Thermofilum.";
RL Stand. Genomic Sci. 10:122-122(2015).
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; CP009961; AKG39437.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A0F7FJ55; -.
DR STRING; 1550241.MA03_07680; -.
DR KEGG; thf:MA03_07680; -.
DR PATRIC; fig|1550241.5.peg.1593; -.
DR HOGENOM; CLU_002886_0_0_2; -.
DR Proteomes; UP000067434; Chromosome.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:InterPro.
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; 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; IPR003593; AAA+_ATPase.
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 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; 1.
DR Pfam; PF01751; Toprim; 1.
DR Pfam; PF17915; zf_Rg; 1.
DR PRINTS; PR00417; PRTPISMRASEI.
DR SMART; SM00382; AAA; 1.
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|ARBA:ARBA00022840, ECO:0000256|HAMAP-
KW Rule:MF_01125}; 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}; Reference proteome {ECO:0000313|Proteomes:UP000067434};
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 102..265
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000259|PROSITE:PS51192"
FT DOMAIN 648..831
FT /note="Toprim"
FT /evidence="ECO:0000259|PROSITE:PS50880"
FT REGION 644..1255
FT /note="Topoisomerase I"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01125"
FT COILED 254..291
FT /evidence="ECO:0000256|SAM:Coils"
FT ACT_SITE 996
FT /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01125"
FT BINDING 98
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01125"
SQ SEQUENCE 1255 AA; 142560 MW; A802B2D93B7AF047 CRC64;
MHAIFRELCP NCGGPVTDQR LENRLPCQVC LPSTKTLRGA PDNLSTPEYV SYMKDLVLRL
EKRGRVGRLG EVVKLEEELS SFIDFFEKAV GSRPWSAQVT WARRVLKGSS FAVLAPTGVG
KTVFGLTMSL YLASKGGKVY LVLPTTTLLG QVYDKALQFA SRVGFDRERI MAYHGGLSPK
EREEVLDRVS RGDYSILLTT AQFLARNFEY LKGARFDFVF VDDVDSVLKS SKNIDRILVL
LGFSEEEIST ALELVTLRAR MLIMQRNRKH AENNADELEK LQSKLESMLA RSGKKGVLVV
STATGRARGQ RVKLFRELLG FEVGSRSEQL RNVLDVYALS SELDLTDKAV ELVSTLGPGG
LVFFPIGTPE DKLAKMVERL AARGLKAEYV YGKAKRNLLE RFSSGEVGVL VGVASYYGLL
VRGLDLPHVV KYAVFVGVPR FKFRLVPEEL TPNRLLQLAS NLVSIVEKGD AVEINRLVAN
IRSRILQLDA SQYRALQELY MQGVTNGRYA FLVKSLLRLR DLVVKYLSDP SVLERLSEET
TVKMFREEGQ YYVILPDVYT YLQASGRTSR LYAGGISKGL SIILENDAVL LEKFFRAIRF
YTGESQWKKL EEVDLGRTME EVSREREVIK AIIEGRASAA LAKDLVKSVL VIVESPTKAK
TIASFFGKPN RRRMGSLFVY ETTTGNRILQ IVASQGHVYD LITSTEFFFK NYSLNKYGVL
VNPEKNAFVP VFTSLKKCLD CGRQFTDYKA DGNTYNVGGK GSTLKRCPYC GSDRVVDKMD
LVLKLQDLAY EVDEVLLATD PDTEGEKIAW DIYVTLKPFT RVLRRIEFHE ITRKAFQEAL
DNPRDVNMNL VKSQFVRRIE DRWVGFALSK KLQENFGMTW LSAGRVQTPV LGWVIDRYRE
SMKSVRPVFK VVLENNVYLI IEDVQLDGKR PSIVAKALQG SEVIVEEKAT EEKLLNPPPP
YTTDTMLRDA NELLGMSADV AMRVAQQLFE SGLITYHRTD STRVSDAGIN VARTYISEKF
GSEMFTARRW GAEGAHECIR PTRPIDAETL SLQIQQGVIQ LPIQLTRQHF ALYRLIFSRF
MASQMMPARV KEKVVEVKSE YFAKEYRFVA GVVEEGFLKV QPLRQAFRLE PGRYRVVDVD
YKRRPLIPLY SQADIVGLMK EKNIGRPSTY AEIIRKLFAR NYVIEVKGGK LVPTNLGQRV
YQFLYDNFRD YISEDTTKNI LERMDEVEKG ERDYRDVLKE FYGELLKIEE TRCRV
//
