RGYR1_AERPE
ID RGYR1_AERPE Reviewed; 1370 AA.
AC Q9YCB6;
DT 16-FEB-2004, integrated into UniProtKB/Swiss-Prot.
DT 26-JUN-2007, sequence version 2.
DT 03-AUG-2022, entry version 135.
DE RecName: Full=Reverse gyrase 1 {ECO:0000255|HAMAP-Rule:MF_01125};
DE Includes:
DE RecName: Full=Helicase {ECO:0000255|HAMAP-Rule:MF_01125};
DE EC=3.6.4.12 {ECO:0000255|HAMAP-Rule:MF_01125};
DE Includes:
DE RecName: Full=Topoisomerase {ECO:0000255|HAMAP-Rule:MF_01125};
DE EC=5.6.2.2 {ECO:0000255|HAMAP-Rule:MF_01125};
GN Name=rgy1 {ECO:0000255|HAMAP-Rule:MF_01125}; OrderedLocusNames=APE_1340.1;
OS Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 /
OS K1).
OC Archaea; Crenarchaeota; Thermoprotei; Desulfurococcales;
OC Desulfurococcaceae; Aeropyrum.
OX NCBI_TaxID=272557;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1;
RX PubMed=10382966; DOI=10.1093/dnares/6.2.83;
RA Kawarabayasi Y., Hino Y., Horikawa H., Yamazaki S., Haikawa Y., Jin-no K.,
RA Takahashi M., Sekine M., Baba S., Ankai A., Kosugi H., Hosoyama A.,
RA Fukui S., Nagai Y., Nishijima K., Nakazawa H., Takamiya M., Masuda S.,
RA Funahashi T., Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A.,
RA Aoki K., Kubota K., Nakamura Y., Nomura N., Sako Y., Kikuchi H.;
RT "Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon,
RT Aeropyrum pernix K1.";
RL DNA Res. 6:83-101(1999).
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. {ECO:0000255|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; EC=3.6.4.12;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01125};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP-dependent breakage, passage and rejoining of double-
CC stranded DNA.; EC=5.6.2.2; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01125};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01125};
CC Note=Binds two Mg(2+) per subunit. {ECO:0000255|HAMAP-Rule:MF_01125};
CC -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_01125}.
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.
CC {ECO:0000255|HAMAP-Rule:MF_01125}.
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:0000255|HAMAP-Rule:MF_01125}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the prokaryotic type
CC I/III topoisomerase family. {ECO:0000255|HAMAP-Rule:MF_01125}.
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DR EMBL; BA000002; BAA80332.2; -; Genomic_DNA.
DR PIR; F72609; F72609.
DR AlphaFoldDB; Q9YCB6; -.
DR SMR; Q9YCB6; -.
DR STRING; 272557.APE_1340.1; -.
DR PRIDE; Q9YCB6; -.
DR EnsemblBacteria; BAA80332; BAA80332; APE_1340.1.
DR KEGG; ape:APE_1340.1; -.
DR PATRIC; fig|272557.25.peg.915; -.
DR eggNOG; arCOG01526; Archaea.
DR Proteomes; UP000002518; 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: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; cd00186; TOP1Ac; 1.
DR CDD; cd03361; TOPRIM_TopoIA_RevGyr; 1.
DR Gene3D; 1.10.290.10; -; 1.
DR Gene3D; 1.10.460.10; -; 1.
DR Gene3D; 3.40.50.300; -; 3.
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; 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 PANTHER; PTHR43505; PTHR43505; 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; SM00490; HELICc; 1.
DR SMART; SM00437; TOP1Ac; 1.
DR SMART; SM00436; TOP1Bc; 1.
DR SMART; SM00493; TOPRIM; 1.
DR SUPFAM; SSF52540; SSF52540; 2.
DR SUPFAM; SSF56712; SSF56712; 1.
DR TIGRFAMs; TIGR01054; rgy; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS50880; TOPRIM; 1.
PE 3: Inferred from homology;
KW ATP-binding; DNA-binding; Helicase; Hydrolase; Isomerase; Magnesium;
KW Metal-binding; Nucleotide-binding; Reference proteome; Repeat;
KW Topoisomerase; Zinc; Zinc-finger.
FT CHAIN 1..1370
FT /note="Reverse gyrase 1"
FT /id="PRO_0000158084"
FT DOMAIN 99..287
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT DOMAIN 647..825
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT ZN_FING 16..37
FT /note="C4-type 1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT ZN_FING 747..764
FT /note="C4-type 2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT REGION 653..1370
FT /note="Topoisomerase I"
FT MOTIF 220..223
FT /note="DEAD box"
FT ACT_SITE 1028
FT /note="For DNA cleavage activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 95
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 112..119
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 653
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 794
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 794
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 796
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
SQ SEQUENCE 1370 AA; 154734 MW; 03F731FB2EA80936 CRC64;
MASARAASRG VYRYLCPNCG GPNSEERLSR GLPCPRCLPR LPRKGVSGWT GLARLLRREG
TLGAGVKAMA SLEEEARSLW RFFEKAVGSP PWGAQRTWAK RLARGDSFSI IAPTGVGKTT
FGAAASLFYA CKKGMRSYIV LPTTTLAANV ARKLESMVES TGCGRVRLLV IHSKLKTSER
REAMERFEKG DFDILVTTAA FARKYADRLS GYRFRLVFVD DVDAVLRSAR SVDAILKIVG
FDEEAIEKGL EVLRLQREQA RLVGLLQSQR EEVREEARKK LLEVKRRLER LEAEIEARRG
RTASLIVSSA TGRPRGARVR LFRVLLNFEA GGRGDIGLRR VIDSYTHPTD GVAEKVVELV
RRLGTGGLVY VPIDMGVEYA ERLAEELRRA GVKAEAYHAK KPLELLDRFA EGEIDVLVGV
ANYYGTLVRG LDLPARVRYA VFAGVPRHKF GSDIGDPHPS RLLRLLSILA ESRIEEVASA
ARSHMGRLRR MLRVLSPAAL QMIAERVARG EVEGGYDRQV LEAYQFLREA LARDDVWESL
RELDVGIVRE GGRTYILVPD PATYLQASGR TSRLYAGGIT LGLSVVVVDN EPVMRGLMKR
VSWMAEVDWR RFEDLDLQSI LREIDEDREK VRRVVKGLYR GVELVRTALL VVESPNKART
IARFFGQPSV RLLPGGGRVY EVATGDKILM IMASGGHVFD LVVRVDGRDL EAAGGEPEHA
IFGVLRYRLG GNGAAAYTPV YTSIKRCLDC GYQFVDEASR CPRCGSELIR NSLSTVEDLR
RVAWEADEVY VGTDPDTEGE KIGWDVALAL RPYAPDIKRL EFHEVTKKAI LEALSNPRSF
DDNLVDAQVV RRVEDRWIGF TLSPLLWCDF WPRYCKRVLE EYGEKRPHMD RERCAKYKAY
YNLSAGRVQT PTLGWVVDRT LAYRKKVWLY RVVHDSQLLF AVRSDDPEVP ESVKRVLDNW
VKHHKKTGIE PWLDVKAVVE KEEWTALPPP PPYTTDTMLR DANRLLGLGS AEAMRIAQDL
FEWGLITYHR TDSTRVSDRG MQVAREWLET RFGGLAGQLY RPRRWGEGGA HEAIRPVRPI
DVERLQLLVE EGVIELPGTL TRRHLRLYDL IFRRFMASQM READALRVVY RLRVPELDGY
TLTLERVVEI GRPGDAEGVT RGFTLVWPYV RPQPRLVEGR EAWIRARVEG RQVPKAYPYT
EGEIVEEMKT RGIGRPSTYA KIVETLFRRR YVIEVSREEG RGAGFVVATS RGINVYNYLT
EELRSADEEE YGGRIAGILR RVPSLVSEDR TRELERQMDM VEKGDASRDD VLESVFNEIS
DLALLLNIEH PIKHRSRAEG NTQGNTWVSN FVACAVKSPE VSRVWGAGVG
