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Q6F598

- RGYR_THEKO

UniProt

Q6F598 - RGYR_THEKO

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
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    • History
      Entry version 88 (01 Oct 2014)
      Sequence version 1 (16 Aug 2004)
      Previous versions | rss
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    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

    Magnesium. Binds two Mg2+ per subunit By similarity.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

    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

    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.
    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

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    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

    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: October 1, 2014
    This is version 88 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