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Q6F598

- RGYR_THEKO

UniProt

Q6F598 - RGYR_THEKO

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Protein
Reverse gyrase
Gene
rgy, TK0470
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.UniRule annotation

Catalytic activityi

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

Cofactori

Magnesium. Binds two Mg2+ per subunit By similarity.UniRule annotation

Sites

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

Regions

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

Subcellular locationi

GO - Cellular componenti

  1. chromosome Source: InterPro
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 960960Reverse gyrase, 1st part Reviewed prediction
PRO_0000030359Add
BLAST
Chaini961 – 1449489Pko r-Gyr intein Reviewed prediction
PRO_0000030360Add
BLAST
Chaini1450 – 1711262Reverse gyrase, 2nd part Reviewed prediction
PRO_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.UniRule annotation

Keywords - PTMi

Autocatalytic cleavage, Protein splicing

Interactioni

Subunit structurei

Monomer By similarity.UniRule annotation

Protein-protein interaction databases

STRINGi69014.TK0470.

Structurei

3D structure databases

ProteinModelPortaliQ6F598.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini93 – 256164Helicase ATP-binding
Add
BLAST
Domaini642 – 805164Toprim
Add
BLAST
Domaini1160 – 1287128DOD-type homing endonuclease
Add
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni648 – 17111064Topoisomerase IUniRule annotation
Add
BLAST

Motif

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

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.UniRule annotation

Sequence similaritiesi

In the N-terminal section; belongs to the DEAD box helicase family. DDVD subfamily.
In the C-terminal section; belongs to the prokaryotic type I/III topoisomerase family.
Contains 1 Toprim domain.

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiCOG1110.
HOGENOMiHOG000222775.
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. DNA/RNA_helicase_DEAD/DEAH_N.
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.
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

MKAVYREMCP NCWGRISDER LVMRNPCEEC LDEPVHADSY FQLVSAVRNA     50
LKLRGTLKEW EKIYQLENQT REIEEFFKKA TGFTFWSAQR TWVKRLLKGR 100
SFSIIAPTGM GKSTFGAFMA VWHALKGKKS YIVVPTTPLV IQTVRKIEGI 150
MENANADVRL AYYHGNLRKK EKEEMLERIK NEDYDILVTS AQWLARNYEE 200
VLKGRHFDFI FVDDVDAFLK ASKNIDRSLY LLGFTDEIIQ KAWEIIRLKK 250
QMSRYLNGNS EDRNEKLNGL NREIEKLQRE IEKFKRKNKI GIMIIASATG 300
SARGDRIKLY RELLGFEVGS GRSALRNVVD SYLKPTKDIK EHVEELLTRL 350
GKGGLIFVPV DQGLGYAEEL ANYLSEKGFK IELVSSKNKK ALEKFENGEA 400
DYLIGSATYY GSLVRGIDLP HLIRYAVFTG VPKFRFSIDL ERPTIYRALG 450
LLSEIMDFLS EEDRRQAEKL HARLRRLIRN IPQFELLKIE EALAEGLPIE 500
NEFHNHVLGV FRELVEFLRR VLRDEEVLRK LAEDPFISLV KEEGKWYIEI 550
PDVRTYIQAT GRTSRLFAGG ITKGLSVLIV DNEKVFNGLV RQMRWRFQEF 600
KMVPFEELDL DEILRQIDED REKVRLVMEG KISAKVKDLV RSALMIVESP 650
NKARTIANFF GQPSKTRIGD LVAYEISVGD RMLTILASGG HMFDLVTNEG 700
YHGVLIQNEG DMLKFIPVYD TLKRCRDCGH QFVDWEKKGV CPRCGSTNVR 750
DALENVIAMR EIAQEVDEIL IATDPDTEGE KIAWDIRNVL APYTPNIKRI 800
EFHEVTRPAI MKAIQEARDV NENRVNAQIV RRIEDRWIGF ELSQELQRVF 850
ESYNLSAGRV QTPVLGWIIE RYKEFTESEV YFLGLTLENG LQVTIELGKD 900
GKDVEPPEYV TVEEVQLEER ELNPAPPYTT DAMLKDASTF LKLSAPETMR 950
LAQDLFEAGL CVTPDTLVSL ADGRIMEIKD AVEKSEGNLL SVNGLKPKEA 1000
KALKFWEIDW NGPLKVIKLK NGHEIKATPD HGLLVMREGK LGWVSAKNVR 1050
EGDYVAFAYN TGHRGRDEYT LLKLMIKLGI TDVMVELDEE YFNEKVAPIV 1100
RERISTSTKY KYLRRRVLPL YLLQEWGLDD YEAHVKSLYR QRAGSKPIPN 1150
FKLDGRFWYV FGLVLGDGTL RDSKVLISQT PLKDVKSVLE DVFPFLRVFE 1200
TTNQVGFSNS IIAEVFRRLG ARKGKLHPLV FGLREEYINA MIAGYFDTDG 1250
TFSILNDRKG PNFRGILTSK RGDVLRMLSV YLYQIGIMNY LRRDERTGVW 1300
DLIISNRSLE KFREKIYPYL RIRRAQFDEA YSVYRASRRA FEGDLLPVAP 1350
VFGKLKFKNG TKNRILKETG IDVWNWLKRP EGEIPRDKLS KVLEYAEESP 1400
EKEFLKSLVE AGVTWVKVKG VEEELYTGKL YDFTTTTENF LSNGAVSHNC 1450
TYHRTDSTHV SNTGIEVAKE YITQELGEKY FKPRPWGEEG AHEAIRPTRP 1500
IDTGRLMQLI RDGIIQLPRN LTRNHYRLYD MIFRRFMTSQ MTPAKILYEK 1550
AVINAGVGKA ELEGYVEIIE DGWTRLRSPP LRELPKLEKG MKLKVVEAKK 1600
WKAPKVSLYT QGDIIALMKE RKIGRPSTYA KIVETLMRRG YVVETKGRKK 1650
LLPTEKGIKV YHYLVSKYRD LVSEERTREL EEIMDRIEEG IEDYIKVLGE 1700
LYSEIQRYVS G 1711
Length:1,711
Mass (Da):197,560
Last modified:August 16, 2004 - v1
Checksum:i73F19BBF5409E127
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
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.
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. DNA/RNA_helicase_DEAD/DEAH_N.
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.
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: September 3, 2014
This is version 87 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

Similar proteinsi