RGYR_PYRAE
ID RGYR_PYRAE Reviewed; 1228 AA.
AC Q8ZXT5;
DT 16-FEB-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 124.
DE RecName: Full=Reverse gyrase {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=rgy {ECO:0000255|HAMAP-Rule:MF_01125}; OrderedLocusNames=PAE1108;
OS Pyrobaculum aerophilum (strain ATCC 51768 / DSM 7523 / JCM 9630 / CIP
OS 104966 / NBRC 100827 / IM2).
OC Archaea; Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae;
OC Pyrobaculum.
OX NCBI_TaxID=178306;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2;
RX PubMed=11792869; DOI=10.1073/pnas.241636498;
RA Fitz-Gibbon S.T., Ladner H., Kim U.-J., Stetter K.O., Simon M.I.,
RA Miller J.H.;
RT "Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum
RT aerophilum.";
RL Proc. Natl. Acad. Sci. U.S.A. 99:984-989(2002).
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; AE009441; AAL63261.1; -; Genomic_DNA.
DR AlphaFoldDB; Q8ZXT5; -.
DR SMR; Q8ZXT5; -.
DR STRING; 178306.PAE1108; -.
DR EnsemblBacteria; AAL63261; AAL63261; PAE1108.
DR KEGG; pai:PAE1108; -.
DR PATRIC; fig|178306.9.peg.822; -.
DR eggNOG; arCOG01526; Archaea.
DR HOGENOM; CLU_002886_0_0_2; -.
DR InParanoid; Q8ZXT5; -.
DR OMA; GVATYYG; -.
DR Proteomes; UP000002439; 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; 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; 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; Topoisomerase; Zinc;
KW Zinc-finger.
FT CHAIN 1..1228
FT /note="Reverse gyrase"
FT /id="PRO_0000158088"
FT DOMAIN 92..255
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT DOMAIN 635..809
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT ZN_FING 12..33
FT /note="C4-type"
FT /evidence="ECO:0000250"
FT REGION 641..1228
FT /note="Topoisomerase I"
FT MOTIF 211..214
FT /note="DEAD box"
FT ACT_SITE 967
FT /note="For DNA cleavage activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 88
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 105..112
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 641
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 778
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 778
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 780
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
SQ SEQUENCE 1228 AA; 138352 MW; 78D49EE68AF00728 CRC64;
MEVPLVAYLH SCPNCGGPIT SDRLASGLPC RECLPDGAKA GSIKQVITAL RKRKALQGLA
WVEAYLRGYE EFAEFFKRIV GFEMWGAQRL WARRFVRGKS FAIVAPTGSG KTTFILIATL
YSAKQGKRAL LIFPTSALAH QAYKKLLTFA ERGGVSLKAL AYHSLLTERE KKEALEALER
GDFDVLVTTS AFLPKRFELL SRYKFDFVAA DDVDSILRAT SKNIDRILRL LGVSDAVLNT
ALEVINLTKQ LRKAEVAGDL KEVERLDQEM AKLRAKLREE VQRLKLGVFV ASGALAKARR
TVRLLLFREI LGFDVGGRAE GLRNVVDLYV EASDNVIEQT LALVKRLGPG GIIYVQDREL
GEAIVERARE AGLAVEHFFR PRRGVLESFE RGELAALVGL ASSRSALVRG IDLPHVIRYV
IFVGVPKFKF RVRLEEFSIP AYLTFLYNVR SVLAGDARYK ADRLIGQLKR LAPYALSVQE
ALKKASEGAE LSSFDRHAVD VVKSAVEFVN SLLQNEEIRK AIETSSEVKL AYIDGEMYVL
VPDVTTYIQG SGRTSRLYAG GLSKGLSVVI VDDPKVFHAL KRELSLRFDE AEFKHLGEAD
LDKILADVDR DRKTIRDIME GRLVPAARGV DLMRTILMVV ESPTKARTIA NFFGRPSLII
SEGIPIYEVS TGDAVLMVTA SLGHIYELPT SLNKIDQRQR EVLAKWFGDF KHGNYDGENY
AVIVKEYGFV PVYNKIWRCR GAVYVDDIDI PPGCKPLDVL EAIRNIAVEV DTVLLGTDPD
SEGEKIAFDL YLGLRPYVQD IRRVEFHEVT RRAILNALAN PRGVNFSLVK AQIVRRVEDR
WIGFGLSKIL QANFKNPNLS AGRVQTPVLG WIVNTYEESL KNRVYNVELQ LNDVDIRLQV
PRDVLDVLRK KKRVAIKLVA RERRQVNPPP PYTTDELLRD AVNKLGLSAD YAMRLAQDLF
ESGLITYHRT DSTRVSTAGI AIAREYIVRK FGEGVFKPRS WGEAEEGAHE AIRPTRPIDV
EELRGLVNAG VIQLAIQLTK SHYQLYDIIF RRFMASQMEP SVVEVAKYNV EIDGHVIQLE
RTVGVAYMGF QTLYQLTPVE PELPTGTLDV VIKRYRVVRR VLSQADVLAL MRQRGIGRPS
TYAHILQVLA KRYYVYVTGR TKLMIPTKRG REIFRFLKEA FGKLVSEDRT RLIEQYMDAI
EVGKARYEEV IAELYDEFRK EVLPHLAS
