RGYR_THEMA
ID RGYR_THEMA Reviewed; 1104 AA.
AC O51934;
DT 16-FEB-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1998, sequence version 1.
DT 03-AUG-2022, entry version 154.
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}; Synonyms=topR;
GN OrderedLocusNames=TM_0173;
OS Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826
OS / MSB8).
OC Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga.
OX NCBI_TaxID=243274;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND CHARACTERIZATION.
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=9440516; DOI=10.1128/jb.180.2.274-281.1998;
RA Bouthier de la Tour C., Portemer C., Kaltoum H., Duguet M.;
RT "Reverse gyrase from the hyperthermophilic bacterium Thermotoga maritima:
RT properties and gene structure.";
RL J. Bacteriol. 180:274-281(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=10360571; DOI=10.1038/20601;
RA Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H.,
RA Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A., McDonald L.A.,
RA Utterback T.R., Malek J.A., Linher K.D., Garrett M.M., Stewart A.M.,
RA Cotton M.D., Pratt M.S., Phillips C.A., Richardson D.L., Heidelberg J.F.,
RA Sutton G.G., Fleischmann R.D., Eisen J.A., White O., Salzberg S.L.,
RA Smith H.O., Venter J.C., Fraser C.M.;
RT "Evidence for lateral gene transfer between Archaea and Bacteria from
RT genome sequence of Thermotoga maritima.";
RL Nature 399:323-329(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.
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.
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; AF013268; AAC01563.1; -; Genomic_DNA.
DR EMBL; AE000512; AAD35266.1; -; Genomic_DNA.
DR PIR; C72409; C72409.
DR RefSeq; NP_227988.1; NC_000853.1.
DR RefSeq; WP_004082808.1; NZ_CP011107.1.
DR PDB; 3P4X; X-ray; 2.41 A; A/B=59-541.
DR PDB; 3P4Y; X-ray; 3.20 A; A=59-541.
DR PDB; 4DDT; X-ray; 3.20 A; A=1-1104.
DR PDB; 4DDU; X-ray; 3.00 A; A=1-1104.
DR PDB; 4DDV; X-ray; 3.46 A; A/B=1-1104.
DR PDB; 4DDW; X-ray; 3.90 A; A=1-1104.
DR PDB; 4DDX; X-ray; 4.17 A; A/B=1-1104.
DR PDBsum; 3P4X; -.
DR PDBsum; 3P4Y; -.
DR PDBsum; 4DDT; -.
DR PDBsum; 4DDU; -.
DR PDBsum; 4DDV; -.
DR PDBsum; 4DDW; -.
DR PDBsum; 4DDX; -.
DR AlphaFoldDB; O51934; -.
DR SMR; O51934; -.
DR STRING; 243274.THEMA_03935; -.
DR PRIDE; O51934; -.
DR EnsemblBacteria; AAD35266; AAD35266; TM_0173.
DR KEGG; tma:TM0173; -.
DR eggNOG; COG1110; Bacteria.
DR InParanoid; O51934; -.
DR OMA; GVATYYG; -.
DR OrthoDB; 223233at2; -.
DR EvolutionaryTrace; O51934; -.
DR Proteomes; UP000008183; 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; PS51194; HELICASE_CTER; 1.
DR PROSITE; PS50880; TOPRIM; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; DNA-binding; Helicase; Hydrolase; Isomerase;
KW Magnesium; Metal-binding; Nucleotide-binding; Reference proteome; Repeat;
KW Topoisomerase; Zinc; Zinc-finger.
FT CHAIN 1..1104
FT /note="Reverse gyrase"
FT /id="PRO_0000158082"
FT DOMAIN 87..242
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT DOMAIN 300..522
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT DOMAIN 542..699
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT ZN_FING 11..32
FT /note="C4-type 1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT ZN_FING 621..638
FT /note="C4-type 2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT REGION 548..1104
FT /note="Topoisomerase I"
FT MOTIF 203..206
FT /note="DEAD box"
FT ACT_SITE 851
FT /note="For DNA cleavage activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 83
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 100..107
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 548
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 668
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 668
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 670
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT TURN 12..14
FT /evidence="ECO:0007829|PDB:4DDU"
FT HELIX 20..23
FT /evidence="ECO:0007829|PDB:4DDU"
FT TURN 24..26
FT /evidence="ECO:0007829|PDB:4DDU"
FT TURN 30..32
FT /evidence="ECO:0007829|PDB:4DDU"
FT HELIX 41..47
FT /evidence="ECO:0007829|PDB:4DDU"
FT HELIX 61..75
FT /evidence="ECO:0007829|PDB:3P4X"
FT HELIX 81..91
FT /evidence="ECO:0007829|PDB:3P4X"
FT STRAND 95..99
FT /evidence="ECO:0007829|PDB:3P4X"
FT HELIX 106..117
FT /evidence="ECO:0007829|PDB:3P4X"
FT TURN 118..121
FT /evidence="ECO:0007829|PDB:3P4X"
FT STRAND 124..130
FT /evidence="ECO:0007829|PDB:3P4X"
FT HELIX 131..144
FT /evidence="ECO:0007829|PDB:3P4X"
FT STRAND 151..153
FT /evidence="ECO:0007829|PDB:3P4X"
FT HELIX 160..172
FT /evidence="ECO:0007829|PDB:3P4X"
FT STRAND 176..181
FT /evidence="ECO:0007829|PDB:3P4X"
FT HELIX 182..187
FT /evidence="ECO:0007829|PDB:3P4X"
FT HELIX 189..192
FT /evidence="ECO:0007829|PDB:3P4X"
FT STRAND 198..203
FT /evidence="ECO:0007829|PDB:3P4X"
FT HELIX 205..208
FT /evidence="ECO:0007829|PDB:3P4X"
FT HELIX 212..221
FT /evidence="ECO:0007829|PDB:3P4X"
FT HELIX 226..237
FT /evidence="ECO:0007829|PDB:3P4X"
FT STRAND 252..259
FT /evidence="ECO:0007829|PDB:3P4X"
FT HELIX 265..273
FT /evidence="ECO:0007829|PDB:3P4X"
FT STRAND 274..276
FT /evidence="ECO:0007829|PDB:4DDT"
FT STRAND 288..295
FT /evidence="ECO:0007829|PDB:3P4X"
FT HELIX 298..308
FT /evidence="ECO:0007829|PDB:3P4X"
FT STRAND 310..318
FT /evidence="ECO:0007829|PDB:3P4X"
FT HELIX 319..331
FT /evidence="ECO:0007829|PDB:3P4X"
FT STRAND 336..341
FT /evidence="ECO:0007829|PDB:3P4X"
FT HELIX 343..352
FT /evidence="ECO:0007829|PDB:3P4X"
FT STRAND 356..362
FT /evidence="ECO:0007829|PDB:3P4X"
FT HELIX 367..370
FT /evidence="ECO:0007829|PDB:3P4X"
FT TURN 375..377
FT /evidence="ECO:0007829|PDB:3P4X"
FT STRAND 380..385
FT /evidence="ECO:0007829|PDB:3P4X"
FT STRAND 388..392
FT /evidence="ECO:0007829|PDB:4DDU"
FT STRAND 394..397
FT /evidence="ECO:0007829|PDB:4DDU"
FT HELIX 400..410
FT /evidence="ECO:0007829|PDB:4DDU"
FT HELIX 420..430
FT /evidence="ECO:0007829|PDB:4DDU"
FT HELIX 434..444
FT /evidence="ECO:0007829|PDB:4DDU"
FT STRAND 447..451
FT /evidence="ECO:0007829|PDB:4DDU"
FT TURN 452..455
FT /evidence="ECO:0007829|PDB:4DDU"
FT STRAND 456..460
FT /evidence="ECO:0007829|PDB:4DDU"
FT HELIX 462..470
FT /evidence="ECO:0007829|PDB:3P4X"
FT STRAND 475..478
FT /evidence="ECO:0007829|PDB:3P4Y"
FT STRAND 483..488
FT /evidence="ECO:0007829|PDB:3P4X"
FT HELIX 492..505
FT /evidence="ECO:0007829|PDB:3P4X"
FT STRAND 510..512
FT /evidence="ECO:0007829|PDB:3P4X"
FT HELIX 513..515
FT /evidence="ECO:0007829|PDB:3P4X"
FT HELIX 518..532
FT /evidence="ECO:0007829|PDB:3P4X"
FT STRAND 543..548
FT /evidence="ECO:0007829|PDB:4DDU"
FT HELIX 550..560
FT /evidence="ECO:0007829|PDB:4DDU"
FT STRAND 564..568
FT /evidence="ECO:0007829|PDB:4DDU"
FT STRAND 571..578
FT /evidence="ECO:0007829|PDB:4DDU"
FT STRAND 581..587
FT /evidence="ECO:0007829|PDB:4DDU"
FT STRAND 593..595
FT /evidence="ECO:0007829|PDB:4DDU"
FT STRAND 597..599
FT /evidence="ECO:0007829|PDB:4DDU"
FT STRAND 604..607
FT /evidence="ECO:0007829|PDB:4DDU"
FT STRAND 610..612
FT /evidence="ECO:0007829|PDB:4DDU"
FT STRAND 614..617
FT /evidence="ECO:0007829|PDB:4DDU"
FT STRAND 619..621
FT /evidence="ECO:0007829|PDB:4DDU"
FT TURN 622..624
FT /evidence="ECO:0007829|PDB:4DDU"
FT TURN 636..638
FT /evidence="ECO:0007829|PDB:4DDU"
FT STRAND 643..645
FT /evidence="ECO:0007829|PDB:4DDU"
FT HELIX 646..656
FT /evidence="ECO:0007829|PDB:4DDU"
FT TURN 657..659
FT /evidence="ECO:0007829|PDB:4DDU"
FT STRAND 661..665
FT /evidence="ECO:0007829|PDB:4DDU"
FT HELIX 671..684
FT /evidence="ECO:0007829|PDB:4DDU"
FT TURN 685..687
FT /evidence="ECO:0007829|PDB:4DDU"
FT STRAND 691..693
FT /evidence="ECO:0007829|PDB:4DDU"
FT STRAND 697..700
FT /evidence="ECO:0007829|PDB:4DDU"
FT HELIX 701..709
FT /evidence="ECO:0007829|PDB:4DDU"
FT HELIX 716..744
FT /evidence="ECO:0007829|PDB:4DDU"
FT HELIX 753..767
FT /evidence="ECO:0007829|PDB:4DDU"
FT TURN 768..771
FT /evidence="ECO:0007829|PDB:4DDU"
FT STRAND 776..781
FT /evidence="ECO:0007829|PDB:4DDU"
FT STRAND 786..791
FT /evidence="ECO:0007829|PDB:4DDU"
FT STRAND 797..810
FT /evidence="ECO:0007829|PDB:4DDU"
FT HELIX 818..828
FT /evidence="ECO:0007829|PDB:4DDU"
FT HELIX 833..845
FT /evidence="ECO:0007829|PDB:4DDU"
FT STRAND 848..850
FT /evidence="ECO:0007829|PDB:4DDU"
FT HELIX 861..874
FT /evidence="ECO:0007829|PDB:4DDU"
FT HELIX 877..879
FT /evidence="ECO:0007829|PDB:4DDU"
FT STRAND 896..899
FT /evidence="ECO:0007829|PDB:4DDU"
FT HELIX 902..911
FT /evidence="ECO:0007829|PDB:4DDU"
FT HELIX 919..936
FT /evidence="ECO:0007829|PDB:4DDU"
FT STRAND 940..953
FT /evidence="ECO:0007829|PDB:4DDU"
FT STRAND 955..966
FT /evidence="ECO:0007829|PDB:4DDU"
FT HELIX 969..971
FT /evidence="ECO:0007829|PDB:4DDU"
FT STRAND 983..994
FT /evidence="ECO:0007829|PDB:4DDU"
FT HELIX 1004..1014
FT /evidence="ECO:0007829|PDB:4DDU"
FT TURN 1019..1021
FT /evidence="ECO:0007829|PDB:4DDU"
FT HELIX 1022..1031
FT /evidence="ECO:0007829|PDB:4DDU"
FT STRAND 1034..1037
FT /evidence="ECO:0007829|PDB:4DDU"
FT STRAND 1043..1045
FT /evidence="ECO:0007829|PDB:4DDU"
FT HELIX 1047..1059
FT /evidence="ECO:0007829|PDB:4DDU"
FT HELIX 1061..1063
FT /evidence="ECO:0007829|PDB:4DDU"
FT HELIX 1066..1080
FT /evidence="ECO:0007829|PDB:4DDU"
FT HELIX 1086..1100
FT /evidence="ECO:0007829|PDB:4DDU"
SQ SEQUENCE 1104 AA; 128277 MW; C493932C2BFDAA12 CRC64;
MAVNSKYHHS CINCGGLNTD ERNERGLPCE VCLPEDSPSD IYRALLERKT LKEYRFYHEF
WNEYEDFRSF FKKKFGKDLT GYQRLWAKRI VQGKSFTMVA PTGVGKTTFG MMTALWLARK
GKKSALVFPT VTLVKQTLER LQKLADEKVK IFGFYSSMKK EEKEKFEKSF EEDDYHILVF
STQFVSKNRE KLSQKRFDFV FVDDVDAVLK ASRNIDTLLM MVGIPEEIIR KAFSTIKQGK
IYERPKNLKP GILVVSSATA KPRGIRPLLF RDLLNFTVGR LVSVARNITH VRISSRSKEK
LVELLEIFRD GILIFAQTEE EGKELYEYLK RFKFNVGETW SEFEKNFEDF KVGKINILIG
VQAYYGKLTR GVDLPERIKY VIFWGTPSMR FSLELDKAPR FVLARVLKEM GLIKAQENPD
VEELRKIAKE HLTQKEFVEK VKEMFRGVVV KDEDLELIIP DVYTYIQASG RSSRILNGVL
VKGVSVIFEE DEEIFESLKT RLLLIAEEEI IEEAEANWKE LVHEVEESRR RSERELTDTS
RSLLIIVESP TKAETLSRFL GRASSRKERN IIVHEAVTGE GVILFTATRG HVYDLVTKGG
IHGVEEENGK FVPVYNSLKR CRDCGYQFTE DRDECPVCSS KNIDDKTETL RALREISLEA
DEILVATDPD VEGEKISWDV TQYLLPSTRS LRRIEMHEIT RYGFKKARES VRFVDFNLVK
AQIVRRVQDR WIGFELSGKL QKRFGRSNLS AGRVQSTVLG WIVEREEEYK KSEKDFTLLV
LENGVNLEVE GKIADDVVTV VELQEAEEEK NPLPPYTTSS ALSEISQKLR LGVQEVMDIL
QDLFEKGFIT YHRTDSTRIS LEGQNVARTY LRKIGKEDIF MGRSWSTEGA HEAIRPVKPI
DARELEEMIE EGLIADLTKK HLRVYELIFN RFLASQSAAV KVKKQIVTVD VDGKRMGIEQ
IVEILRDGWN LFVPLTVSPR FEHRTYKIKE KKFYKKHTVP LFTQASIVEE MKKRGIGRPS
TYAKIVEVLF RRGYVYEDKY KRVRPTRFGV MVYSYLKERY EKYVTEETTR RLEEIMDKVE
RGEEDYQATL RLLYEEIKSL MEEG
