ID RGYR_CALS4 Reviewed; 1117 AA.
AC Q8R979;
DT 16-FEB-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 1.
DT 27-MAR-2024, entry version 133.
DE RecName: Full=Reverse gyrase {ECO:0000255|HAMAP-Rule:MF_01125};
DE Short=TtRG {ECO:0000303|PubMed:21318561};
DE EC=5.6.2.- {ECO:0000255|HAMAP-Rule:MF_01125, ECO:0000269|PubMed:21318561};
GN Name=rgy {ECO:0000255|HAMAP-Rule:MF_01125}; OrderedLocusNames=TTE1745;
OS Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM
OS 11007 / NBRC 100824 / MB4) (Thermoanaerobacter tengcongensis).
OC Bacteria; Bacillota; Clostridia; Thermoanaerobacterales;
OC Thermoanaerobacteraceae; Caldanaerobacter.
OX NCBI_TaxID=273068;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 15242 / JCM 11007 / NBRC 100824 / MB4;
RX PubMed=11997336; DOI=10.1101/gr.219302;
RA Bao Q., Tian Y., Li W., Xu Z., Xuan Z., Hu S., Dong W., Yang J., Chen Y.,
RA Xue Y., Xu Y., Lai X., Huang L., Dong X., Ma Y., Ling L., Tan H., Chen R.,
RA Wang J., Yu J., Yang H.;
RT "A complete sequence of the T. tengcongensis genome.";
RL Genome Res. 12:689-700(2002).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVE SITE, BIOPHYSICOCHEMICAL PROPERTIES,
RP DNA-BINDING, AND MUTAGENESIS OF 1-MET--CYS-34; 214-SER--LYS-267;
RP 394-SER--TYR-477; 634-CYS--CYS-651 AND TYR-864.
RC STRAIN=DSM 15242 / JCM 11007 / NBRC 100824 / MB4;
RX PubMed=21318561; DOI=10.1007/s00792-011-0356-5;
RA Li J., Liu J., Zhou J., Xiang H.;
RT "Functional evaluation of four putative DNA-binding regions in
RT Thermoanaerobacter tengcongensis reverse gyrase.";
RL Extremophiles 15:281-291(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; also positively supercoils with dATP and ATP-gamma-S
CC (PubMed:21318561). With UTP or dTTP relaxes negatively supercoiled DNA,
CC in the absence of any nucleotide partially relaxes negative supercoils
CC (PubMed:21318561). In the absence of nucleotide has a higher affinity
CC for dsDNA with a single-stranded tail than dsDNA or ssDNA
CC (PubMed:21318561). Has an ATPase activity in the absence of DNA
CC (PubMed:21318561). Binds to single-stranded DNA, transiently cleaves
CC and then rejoins the ends, introducing a positive supercoil in the
CC process (PubMed:21318561) (Probable). The scissile phosphodiester is
CC attacked by the catalytic tyrosine of the enzyme, resulting in the
CC formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate
CC (PubMed:21318561) (Probable). Probably involved in rewinding DNA
CC strands in regions of the chromosome that have opened up to allow
CC replication, transcription, DNA repair and/or for DNA protection.
CC {ECO:0000269|PubMed:21318561, ECO:0000305|PubMed:21318561}.
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; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01125, ECO:0000269|PubMed:21318561};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01125};
CC Note=Binds 2 zinc ions per subunit. {ECO:0000255|HAMAP-Rule:MF_01125};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01125};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Temperature dependence:
CC Optimum temperature is 75 degrees Celsius for positive supercoiling
CC (PubMed:21318561). Optimum temperature is 60 degrees Celsius for
CC ATPase (PubMed:21318561). No supercoiling is seen below 50 degrees
CC Celsius (PubMed:21318561). {ECO:0000269|PubMed:21318561};
CC -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_01125}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|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:0000255|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:0000255|HAMAP-
CC Rule:MF_01125}.
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 type IA
CC topoisomerase family. {ECO:0000255|HAMAP-Rule:MF_01125}.
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DR EMBL; AE008691; AAM24939.1; -; Genomic_DNA.
DR AlphaFoldDB; Q8R979; -.
DR SMR; Q8R979; -.
DR STRING; 273068.TTE1745; -.
DR KEGG; tte:TTE1745; -.
DR eggNOG; COG1110; Bacteria.
DR HOGENOM; CLU_002886_0_0_9; -.
DR OrthoDB; 9804262at2; -.
DR Proteomes; UP000000555; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
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:0160097; F:reverse gyrase activity; IDA:UniProtKB.
DR GO; GO:0008270; F:zinc ion binding; IMP:UniProtKB.
DR GO; GO:0006265; P:DNA topological change; IDA:UniProtKB.
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; 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; 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; PS52039; TOPO_IA_2; 1.
DR PROSITE; PS50880; TOPRIM; 1.
DR PROSITE; PS52037; ZF_RG_C; 1.
DR PROSITE; PS52036; ZF_RG_N; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Cytoplasm; DNA-binding; Isomerase; Magnesium; Metal-binding;
KW Nucleotide-binding; Reference proteome; Repeat; Topoisomerase; Zinc;
KW Zinc-finger.
FT CHAIN 1..1117
FT /note="Reverse gyrase"
FT /id="PRO_0000158083"
FT DOMAIN 88..284
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT DOMAIN 555..712
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT DOMAIN 728..1114
FT /note="Topo IA-type catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01383"
FT ZN_FING 3..42
FT /note="RG N-terminal-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01380"
FT ZN_FING 631..658
FT /note="RG C-terminal-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01381"
FT REGION 551..1117
FT /note="Topoisomerase I"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT MOTIF 206..209
FT /note="DEAD box"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT ACT_SITE 864
FT /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01383,
FT ECO:0000305|PubMed:21318561"
FT BINDING 13
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 16
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 31
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 34
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 84
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 101..108
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 561
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 634
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 637
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 648
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 651
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 681
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT MUTAGEN 1..34
FT /note="Missing: Loss of positive supercoiling activity,
FT still relaxes negative supercoils, very weak DNA-binding,
FT protein is unstable at 75 degrees Celsius."
FT /evidence="ECO:0000269|PubMed:21318561"
FT MUTAGEN 214..267
FT /note="Missing: Loss of positive supercoiling activity,
FT still relaxes negative supercoils, significant loss of DNA-
FT binding at 75 degrees Celsius, strongly decreased ATPase."
FT /evidence="ECO:0000269|PubMed:21318561"
FT MUTAGEN 394..477
FT /note="Missing: Loss of positive supercoiling activity,
FT still relaxes negative supercoils, improved DNA-binding,
FT nearly complete loss of ATPase."
FT /evidence="ECO:0000269|PubMed:21318561"
FT MUTAGEN 634..651
FT /note="CSSCGAQFTDELPRCPYC->ASSAGAQFTDELPRAPYA: Loss of
FT positive supercoiling activity, still relaxes negative
FT supercoils, very weak DNA-binding, protein is unstable at
FT 75 degrees Celsius."
FT /evidence="ECO:0000269|PubMed:21318561"
FT MUTAGEN 864
FT /note="Y->F: Loss of positive supercoiling activity, does
FT not relax negative supercoils."
FT /evidence="ECO:0000269|PubMed:21318561"
SQ SEQUENCE 1117 AA; 128615 MW; 68D5D6F0820D392F CRC64;
MALATGAKYY HSCINCGGIN TDTRNEKGLP CEVCLPFEDG DVLKGLKLNN SLKGYEKYWN
LNQQYKEFEE FFFSKINKKP TGYQRFWAKR LLLSKSFTLV APTGVGKTTF GLISALWIAK
KGGKVALVFP TVSLVEQAAK RLIEFSKEDE DVNILFYTSS LKKKEREKFE KNFSEGNYDI
LVISSQFISK RKEQLSQKVF DLVFVDDVDA VLKSSKNIDT LLNMIGISQK AIDSTLDNLK
KGNNSDKIQI EEKAPKGRLI VSSATAKPKG IKPLLFRELL GFEIGRFTTS ARNITNVRIK
EKSLEKLLYI INLLKDGILL FVPTEEEGKE IANYLEEHGV KLGKTWEDFE KSFEKFKEGS
LQLLCGIYSY YGKLVRGIDL PLRIKFAVFW GTPSFKFSTK LENAPRFILE RNFQDYLENN
PKLKAYFKDL QRLSTEKLRK SVEKYISPET WEKLIQKNFP TTKFDKEKNL IVIPDVYTYI
QASGRTSRIF GTSLTKGISI LFEEDDSLFE LLKARLLYLT EEEWTEEGEI EHLVKEAEET
RKAISTDSSS KDMKSRMIIV ESPTKAQTIS KFLEKSSTRR YGSLMVHESI TQEGILLLTA
SKGHLYDLET KTGLHGVEIN DGRFIPYYNS IKRCSSCGAQ FTDELPRCPY CNSDKIDDKK
KILEALRDIA MEVDEVIIAT DPDVEGEKIG WDISQYIKPV NKNVQRIEMH EITKFGFDKA
IRNRRNCDVN LVKSQIVRRI EDRWVGFELS LRLQKNFQNS NLSAGRVQST VLGWILEKEI
EHSKSKKTVT QFTLDNGFKF EVDGKIDVDE VEVEIVEEKE QALSPLPPFN TPSLLTAASQ
QFKLPVQQIM EILQTLFELG FITYHRTDST RISSTGQKIA RSYLEKIGKI TLLSEREWGK
EGAHEAIRPV KPISPEELSE FITEKIAAYL SPMHIKVYSL IFNRFMASQM TSPVVINQKI
LIKNGSFQVE REVPVKLQEE GWNIFNPITV YTPFEEKKYS VVSKRTYTTH TVPLFTQASL
IEEMQKRNIG RPSTYAKIVD ILFKRKYIIE DVYKRLRTTA LGRKVYSYLS ERYMNYINEE
TTRQLEKLME SVETGEKDYQ SVLKNLYEEL NEILIKN
//
