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Protein

Reverse gyrase

Gene

rgy

Organism
Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Status
Reviewed-Annotation score: -Protein inferred from homologyi

Functioni

Modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. It cleaves transiently a single DNA strand and remains covalently bound to the 5' DNA end through a tyrosine residue. May be involved in rewinding the DNA strands in the regions of the chromosome that have opened up to allow transcription or replication (By similarity).By similarity

Miscellaneous

This enzyme is the only unique feature of hyperthermophilic bacteria/archaea discovered so far. It appears to be essential for adaptation to life at high temperatures.

Catalytic activityi

ATP + H2O = ADP + phosphate.
ATP-dependent breakage, passage and rejoining of double-stranded DNA.

Cofactori

Mg2+By similarityNote: Binds two Mg2+ per subunit.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei89ATPBy similarity1
Metal bindingi648Magnesium 1; catalyticBy similarity1
Metal bindingi774Magnesium 1; catalyticBy similarity1
Metal bindingi774Magnesium 2By similarity1
Metal bindingi776Magnesium 2By similarity1
Active sitei1452For DNA cleavage activityBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri9 – 30C4-type 1By similarityAdd BLAST22
Nucleotide bindingi106 – 113ATPBy similarity8
Zinc fingeri725 – 744C4-type 2By similarityAdd BLAST20

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, Helicase, Hydrolase, Isomerase, Topoisomerase
LigandATP-binding, Magnesium, Metal-binding, Nucleotide-binding, Zinc

Enzyme and pathway databases

BioCyciTKOD69014:G1G2A-467-MONOMER

Names & Taxonomyi

Protein namesi
Recommended name:
Reverse gyrase
Cleaved into the following chain:
Including the following 2 domains:
Helicase (EC:3.6.4.12)
Topoisomerase (EC:5.99.1.3)
Gene namesi
Name:rgy
Ordered Locus Names:TK0470
OrganismiThermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Taxonomic identifieri69014 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
Proteomesi
  • UP000000536 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000303591 – 960Reverse gyrase, 1st partSequence analysisAdd BLAST960
ChainiPRO_0000030360961 – 1449Pko r-Gyr inteinSequence analysisAdd BLAST489
ChainiPRO_00000418801450 – 1711Reverse gyrase, 2nd partSequence analysisAdd BLAST262

Post-translational modificationi

This protein undergoes a protein self splicing that involves a post-translational excision of the intervening region (intein) followed by peptide ligation.By similarity

Keywords - PTMi

Autocatalytic cleavage, Protein splicing

Proteomic databases

PRIDEiQ6F598

Interactioni

Subunit structurei

Monomer.By similarity

Protein-protein interaction databases

STRINGi69014.TK0470

Structurei

3D structure databases

ProteinModelPortaliQ6F598
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini93 – 256Helicase ATP-bindingAdd BLAST164
Domaini642 – 805ToprimAdd BLAST164
Domaini1160 – 1287DOD-type homing endonucleaseAdd BLAST128

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni648 – 1711Topoisomerase IAdd BLAST1064

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi213 – 216DEAD box4

Domaini

Both the DNA unwinding and positive supercoiling activities require the cooperation of both domains. The cooperative action between the helicase-like and the topoisomerase domains is specific. The helicase-like domain probably does not directly unwind DNA but acts more likely by driving ATP-dependent conformational changes within the whole enzyme, functioning more like a protein motor. The "latch" region of the N-terminal domain plays a regulatory role in the enzyme, repressing topoisomerase activity in the absence of ATP and therefore preventing the enzyme from acting as an ATP-independent relaxing enzyme; it also helps to coordinate nucleotide hydrolysis by the ATPase domain with the supercoiling activity of the topoisomerase domain (By similarity).By similarity

Sequence similaritiesi

In the N-terminal section; belongs to the DEAD box helicase family. DDVD subfamily.Curated
In the C-terminal section; belongs to the prokaryotic type I/III topoisomerase family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri9 – 30C4-type 1By similarityAdd BLAST22
Zinc fingeri725 – 744C4-type 2By similarityAdd BLAST20

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiarCOG01526 Archaea
arCOG03151 Archaea
COG1110 LUCA
HOGENOMiHOG000222775
InParanoidiQ6F598
KOiK03170
OMAiGVATYYG
OrthoDBiPOG093Z0046

Family and domain databases

CDDicd00186 TOP1Ac, 1 hit
cd03361 TOPRIM_TopoIA_RevGyr, 1 hit
Gene3Di1.10.290.10, 1 hit
1.10.460.10, 2 hits
3.10.28.10, 1 hit
HAMAPiMF_01125 Reverse_gyrase, 1 hit
InterProiView protein in InterPro
IPR011545 DEAD/DEAH_box_helicase_dom
IPR014001 Helicase_ATP-bd
IPR003586 Hint_dom_C
IPR003587 Hint_dom_N
IPR036844 Hint_dom_sf
IPR027434 Homing_endonucl
IPR030934 Intein_C
IPR004042 Intein_endonuc
IPR006141 Intein_N
IPR004860 LAGLIDADG_2
IPR027417 P-loop_NTPase
IPR005736 Reverse_gyrase
IPR003601 Topo_IA_2
IPR013497 Topo_IA_cen
IPR013824 Topo_IA_cen_sub1
IPR013826 Topo_IA_cen_sub3
IPR023405 Topo_IA_core_domain
IPR003602 Topo_IA_DNA-bd_dom
IPR006171 TOPRIM_domain
IPR034142 TOPRIM_RevGyr
PANTHERiPTHR43505 PTHR43505, 1 hit
PfamiView protein in Pfam
PF00270 DEAD, 1 hit
PF14528 LAGLIDADG_3, 1 hit
PF01131 Topoisom_bac, 2 hits
PF01751 Toprim, 1 hit
PRINTSiPR00417 PRTPISMRASEI
SMARTiView protein in SMART
SM00487 DEXDc, 1 hit
SM00305 HintC, 1 hit
SM00306 HintN, 1 hit
SM00437 TOP1Ac, 1 hit
SM00436 TOP1Bc, 1 hit
SM00493 TOPRIM, 1 hit
SUPFAMiSSF51294 SSF51294, 3 hits
SSF52540 SSF52540, 4 hits
SSF55608 SSF55608, 1 hit
SSF56712 SSF56712, 2 hits
TIGRFAMsiTIGR01443 intein_Cterm, 1 hit
TIGR01445 intein_Nterm, 1 hit
TIGR01054 rgy, 1 hit
PROSITEiView protein in PROSITE
PS51192 HELICASE_ATP_BIND_1, 1 hit
PS50818 INTEIN_C_TER, 1 hit
PS50819 INTEIN_ENDONUCLEASE, 1 hit
PS50817 INTEIN_N_TER, 1 hit
PS50880 TOPRIM, 1 hit

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q6F598-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKAVYREMCP NCWGRISDER LVMRNPCEEC LDEPVHADSY FQLVSAVRNA
60 70 80 90 100
LKLRGTLKEW EKIYQLENQT REIEEFFKKA TGFTFWSAQR TWVKRLLKGR
110 120 130 140 150
SFSIIAPTGM GKSTFGAFMA VWHALKGKKS YIVVPTTPLV IQTVRKIEGI
160 170 180 190 200
MENANADVRL AYYHGNLRKK EKEEMLERIK NEDYDILVTS AQWLARNYEE
210 220 230 240 250
VLKGRHFDFI FVDDVDAFLK ASKNIDRSLY LLGFTDEIIQ KAWEIIRLKK
260 270 280 290 300
QMSRYLNGNS EDRNEKLNGL NREIEKLQRE IEKFKRKNKI GIMIIASATG
310 320 330 340 350
SARGDRIKLY RELLGFEVGS GRSALRNVVD SYLKPTKDIK EHVEELLTRL
360 370 380 390 400
GKGGLIFVPV DQGLGYAEEL ANYLSEKGFK IELVSSKNKK ALEKFENGEA
410 420 430 440 450
DYLIGSATYY GSLVRGIDLP HLIRYAVFTG VPKFRFSIDL ERPTIYRALG
460 470 480 490 500
LLSEIMDFLS EEDRRQAEKL HARLRRLIRN IPQFELLKIE EALAEGLPIE
510 520 530 540 550
NEFHNHVLGV FRELVEFLRR VLRDEEVLRK LAEDPFISLV KEEGKWYIEI
560 570 580 590 600
PDVRTYIQAT GRTSRLFAGG ITKGLSVLIV DNEKVFNGLV RQMRWRFQEF
610 620 630 640 650
KMVPFEELDL DEILRQIDED REKVRLVMEG KISAKVKDLV RSALMIVESP
660 670 680 690 700
NKARTIANFF GQPSKTRIGD LVAYEISVGD RMLTILASGG HMFDLVTNEG
710 720 730 740 750
YHGVLIQNEG DMLKFIPVYD TLKRCRDCGH QFVDWEKKGV CPRCGSTNVR
760 770 780 790 800
DALENVIAMR EIAQEVDEIL IATDPDTEGE KIAWDIRNVL APYTPNIKRI
810 820 830 840 850
EFHEVTRPAI MKAIQEARDV NENRVNAQIV RRIEDRWIGF ELSQELQRVF
860 870 880 890 900
ESYNLSAGRV QTPVLGWIIE RYKEFTESEV YFLGLTLENG LQVTIELGKD
910 920 930 940 950
GKDVEPPEYV TVEEVQLEER ELNPAPPYTT DAMLKDASTF LKLSAPETMR
960 970 980 990 1000
LAQDLFEAGL CVTPDTLVSL ADGRIMEIKD AVEKSEGNLL SVNGLKPKEA
1010 1020 1030 1040 1050
KALKFWEIDW NGPLKVIKLK NGHEIKATPD HGLLVMREGK LGWVSAKNVR
1060 1070 1080 1090 1100
EGDYVAFAYN TGHRGRDEYT LLKLMIKLGI TDVMVELDEE YFNEKVAPIV
1110 1120 1130 1140 1150
RERISTSTKY KYLRRRVLPL YLLQEWGLDD YEAHVKSLYR QRAGSKPIPN
1160 1170 1180 1190 1200
FKLDGRFWYV FGLVLGDGTL RDSKVLISQT PLKDVKSVLE DVFPFLRVFE
1210 1220 1230 1240 1250
TTNQVGFSNS IIAEVFRRLG ARKGKLHPLV FGLREEYINA MIAGYFDTDG
1260 1270 1280 1290 1300
TFSILNDRKG PNFRGILTSK RGDVLRMLSV YLYQIGIMNY LRRDERTGVW
1310 1320 1330 1340 1350
DLIISNRSLE KFREKIYPYL RIRRAQFDEA YSVYRASRRA FEGDLLPVAP
1360 1370 1380 1390 1400
VFGKLKFKNG TKNRILKETG IDVWNWLKRP EGEIPRDKLS KVLEYAEESP
1410 1420 1430 1440 1450
EKEFLKSLVE AGVTWVKVKG VEEELYTGKL YDFTTTTENF LSNGAVSHNC
1460 1470 1480 1490 1500
TYHRTDSTHV SNTGIEVAKE YITQELGEKY FKPRPWGEEG AHEAIRPTRP
1510 1520 1530 1540 1550
IDTGRLMQLI RDGIIQLPRN LTRNHYRLYD MIFRRFMTSQ MTPAKILYEK
1560 1570 1580 1590 1600
AVINAGVGKA ELEGYVEIIE DGWTRLRSPP LRELPKLEKG MKLKVVEAKK
1610 1620 1630 1640 1650
WKAPKVSLYT QGDIIALMKE RKIGRPSTYA KIVETLMRRG YVVETKGRKK
1660 1670 1680 1690 1700
LLPTEKGIKV YHYLVSKYRD LVSEERTREL EEIMDRIEEG IEDYIKVLGE
1710
LYSEIQRYVS G
Length:1,711
Mass (Da):197,560
Last modified:August 16, 2004 - v1
Checksum:i73F19BBF5409E127
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB117612 Genomic DNA Translation: BAD26706.1
AP006878 Genomic DNA Translation: BAD84659.1
RefSeqiWP_011249425.1, NC_006624.1

Genome annotation databases

EnsemblBacteriaiBAD84659; BAD84659; TK0470
GeneIDi3234065
KEGGitko:TK0470
PATRICifig|69014.16.peg.462

Similar proteinsi

Entry informationi

Entry nameiRGYR_THEKO
AccessioniPrimary (citable) accession number: Q6F598
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 30, 2005
Last sequence update: August 16, 2004
Last modified: May 23, 2018
This is version 107 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

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