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Q6F598

- RGYR_THEKO

UniProt

Q6F598 - RGYR_THEKO

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Protein

Reverse gyrase

Gene

rgy

Organism
Thermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Status
Reviewed - Annotation score: 5 out of 5- 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

Catalytic activityi

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

Cofactori

Mg2+By similarityNote: Binds two Mg(2+) per subunit.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei89 – 891ATPBy similarity
Metal bindingi648 – 6481Magnesium 1; catalyticBy similarity
Metal bindingi774 – 7741Magnesium 1; catalyticBy similarity
Metal bindingi774 – 7741Magnesium 2By similarity
Metal bindingi776 – 7761Magnesium 2By similarity
Active sitei1452 – 14521For DNA cleavage activityBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri9 – 3022C4-type 1By similarityAdd
BLAST
Nucleotide bindingi106 – 1138ATPBy similarity
Zinc fingeri725 – 74420C4-type 2By similarityAdd
BLAST

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-HAMAP
  2. DNA binding Source: UniProtKB-HAMAP
  3. DNA topoisomerase type I activity Source: InterPro
  4. DNA topoisomerase type II (ATP-hydrolyzing) activity Source: UniProtKB-HAMAP
  5. endonuclease activity Source: InterPro
  6. helicase activity Source: UniProtKB-HAMAP
  7. magnesium ion binding Source: UniProtKB-HAMAP
  8. zinc ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. DNA topological change Source: UniProtKB-HAMAP
  2. DNA unwinding involved in DNA replication Source: UniProtKB-HAMAP
  3. intein-mediated protein splicing Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase, Isomerase, Topoisomerase

Keywords - Ligandi

ATP-binding, DNA-binding, Magnesium, Metal-binding, Nucleotide-binding, Zinc

Enzyme and pathway databases

BioCyciTKOD69014:GH72-478-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 kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Taxonomic identifieri69014 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
ProteomesiUP000000536: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 960960Reverse gyrase, 1st partSequence AnalysisPRO_0000030359Add
BLAST
Chaini961 – 1449489Pko r-Gyr inteinSequence AnalysisPRO_0000030360Add
BLAST
Chaini1450 – 1711262Reverse gyrase, 2nd partSequence AnalysisPRO_0000041880Add
BLAST

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

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)LengthDescriptionGraphical viewFeature identifierActions
Domaini93 – 256164Helicase ATP-bindingAdd
BLAST
Domaini642 – 805164ToprimAdd
BLAST
Domaini1160 – 1287128DOD-type homing endonucleaseAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni648 – 17111064Topoisomerase IAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi213 – 2164DEAD box

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
Contains 1 helicase ATP-binding domain.Curated
Contains 1 Toprim domain.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri9 – 3022C4-type 1By similarityAdd
BLAST
Zinc fingeri725 – 74420C4-type 2By similarityAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiCOG1110.
HOGENOMiHOG000222775.
InParanoidiQ6F598.
KOiK03170.
OMAiRRMEFHE.

Family and domain databases

Gene3Di1.10.290.10. 2 hits.
1.10.460.10. 2 hits.
2.170.16.10. 2 hits.
3.10.28.10. 1 hit.
3.40.50.140. 1 hit.
3.40.50.300. 4 hits.
HAMAPiMF_01125. Reverse_gyrase.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR028992. Hedgehog/Intein_dom.
IPR014001. Helicase_ATP-bd.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR027434. Homing_endonucl.
IPR004042. Intein_endonuc.
IPR006141. Intein_splice_site.
IPR027417. P-loop_NTPase.
IPR005736. Reverse_gyrase.
IPR000380. Topo_IA.
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.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 1 hit.
PfamiPF00270. DEAD. 1 hit.
PF14528. LAGLIDADG_3. 1 hit.
PF01131. Topoisom_bac. 2 hits.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSiPR00417. PRTPISMRASEI.
SMARTiSM00487. DEXDc. 1 hit.
SM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
SM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
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.
PROSITEiPS51192. 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.
[Graphical view]

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.
YP_182883.1. NC_006624.1.

Genome annotation databases

EnsemblBacteriaiBAD84659; BAD84659; TK0470.
GeneIDi3234065.
KEGGitko:TK0470.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB117612 Genomic DNA. Translation: BAD26706.1 .
AP006878 Genomic DNA. Translation: BAD84659.1 .
RefSeqi WP_011249425.1. NC_006624.1.
YP_182883.1. NC_006624.1.

3D structure databases

ProteinModelPortali Q6F598.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 69014.TK0470.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAD84659 ; BAD84659 ; TK0470 .
GeneIDi 3234065.
KEGGi tko:TK0470.

Phylogenomic databases

eggNOGi COG1110.
HOGENOMi HOG000222775.
InParanoidi Q6F598.
KOi K03170.
OMAi RRMEFHE.

Enzyme and pathway databases

BioCyci TKOD69014:GH72-478-MONOMER.

Family and domain databases

Gene3Di 1.10.290.10. 2 hits.
1.10.460.10. 2 hits.
2.170.16.10. 2 hits.
3.10.28.10. 1 hit.
3.40.50.140. 1 hit.
3.40.50.300. 4 hits.
HAMAPi MF_01125. Reverse_gyrase.
InterProi IPR011545. DEAD/DEAH_box_helicase_dom.
IPR028992. Hedgehog/Intein_dom.
IPR014001. Helicase_ATP-bd.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR027434. Homing_endonucl.
IPR004042. Intein_endonuc.
IPR006141. Intein_splice_site.
IPR027417. P-loop_NTPase.
IPR005736. Reverse_gyrase.
IPR000380. Topo_IA.
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.
[Graphical view ]
PANTHERi PTHR11390. PTHR11390. 1 hit.
Pfami PF00270. DEAD. 1 hit.
PF14528. LAGLIDADG_3. 1 hit.
PF01131. Topoisom_bac. 2 hits.
PF01751. Toprim. 1 hit.
[Graphical view ]
PRINTSi PR00417. PRTPISMRASEI.
SMARTi SM00487. DEXDc. 1 hit.
SM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
SM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view ]
SUPFAMi SSF51294. SSF51294. 3 hits.
SSF52540. SSF52540. 4 hits.
SSF55608. SSF55608. 1 hit.
SSF56712. SSF56712. 2 hits.
TIGRFAMsi TIGR01443. intein_Cterm. 1 hit.
TIGR01445. intein_Nterm. 1 hit.
TIGR01054. rgy. 1 hit.
PROSITEi 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.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Reverse gyrase is not a prerequisite for hyperthermophilic life."
    Atomi H., Matsumi R., Imanaka T.
    J. Bacteriol. 186:4829-4833(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC BAA-918 / JCM 12380 / KOD1.
  2. "Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes."
    Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.
    Genome Res. 15:352-363(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC BAA-918 / JCM 12380 / KOD1.

Entry informationi

Entry nameiRGYR_THEKO
AccessioniPrimary (citable) accession number: Q6F598
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 30, 2005
Last sequence update: August 16, 2004
Last modified: November 26, 2014
This is version 90 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Intein-containing proteins
    List of intein-containing protein entries
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3