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O29238

- RGYR_ARCFU

UniProt

O29238 - RGYR_ARCFU

Protein

Reverse gyrase

Gene

rgy

Organism
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 111 (01 Oct 2014)
      Sequence version 1 (01 Jan 1998)
      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.

    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.UniRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei61 – 611ATP
    Binding sitei84 – 841ATP
    Binding sitei85 – 851ATP
    Binding sitei86 – 861ATP
    Metal bindingi512 – 5121Magnesium 1; catalyticUniRule annotation
    Metal bindingi631 – 6311Magnesium 1; catalyticUniRule annotation
    Metal bindingi631 – 6311Magnesium 2UniRule annotation
    Metal bindingi633 – 6331Magnesium 2UniRule annotation
    Active sitei809 – 8091For DNA cleavage activity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri10 – 2718C4-type 1UniRule annotationAdd
    BLAST
    Nucleotide bindingi78 – 858ATP
    Zinc fingeri584 – 60118C4-type 2UniRule annotationAdd
    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. helicase activity Source: UniProtKB-HAMAP
    6. magnesium ion binding Source: UniProtKB-HAMAP
    7. 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

    Keywords - Molecular functioni

    Helicase, Hydrolase, Isomerase, Topoisomerase

    Keywords - Ligandi

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

    Enzyme and pathway databases

    BioCyciAFUL224325:GJBC-1046-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Reverse gyraseUniRule annotation
    Including the following 2 domains:
    HelicaseUniRule annotation (EC:3.6.4.12UniRule annotation)
    TopoisomeraseUniRule annotation (EC:5.99.1.3UniRule annotation)
    Gene namesi
    Name:rgyUniRule annotation
    Ordered Locus Names:AF_1024
    OrganismiArchaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
    Taxonomic identifieri224325 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaArchaeoglobiArchaeoglobalesArchaeoglobaceaeArchaeoglobus
    ProteomesiUP000002199: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    1. chromosome Source: InterPro

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi809 – 8091Y → F: Loss of topoisomerase activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 10541054Reverse gyrasePRO_0000158086Add
    BLAST

    Interactioni

    Subunit structurei

    Monomer.1 PublicationUniRule annotation

    Protein-protein interaction databases

    STRINGi224325.AF1024.

    Structurei

    Secondary structure

    1
    1054
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi19 – 213
    Helixi40 – 5112
    Turni52 – 543
    Helixi59 – 6911
    Beta strandi74 – 763
    Helixi85 – 9612
    Turni97 – 993
    Beta strandi102 – 1076
    Helixi109 – 12315
    Turni124 – 1263
    Helixi130 – 1323
    Beta strandi133 – 1364
    Helixi144 – 1518
    Helixi153 – 1553
    Beta strandi157 – 1626
    Helixi163 – 1686
    Beta strandi170 – 1734
    Beta strandi177 – 1826
    Helixi184 – 1885
    Helixi192 – 2009
    Beta strandi203 – 2064
    Turni207 – 2104
    Beta strandi211 – 2144
    Beta strandi217 – 2226
    Beta strandi225 – 2273
    Helixi233 – 2408
    Beta strandi254 – 2607
    Turni264 – 2674
    Helixi268 – 2714
    Beta strandi278 – 2847
    Helixi285 – 2939
    Turni294 – 2974
    Beta strandi301 – 3033
    Beta strandi307 – 3093
    Helixi310 – 3167
    Beta strandi321 – 3266
    Helixi327 – 3326
    Helixi334 – 3363
    Turni340 – 3423
    Beta strandi345 – 3506
    Beta strandi353 – 3575
    Turni358 – 3603
    Helixi361 – 3633
    Helixi366 – 3738
    Turni374 – 3763
    Helixi379 – 3835
    Turni387 – 3893
    Helixi393 – 40412
    Beta strandi412 – 4176
    Beta strandi420 – 4245
    Helixi426 – 4349
    Beta strandi447 – 4526
    Helixi456 – 46712
    Helixi481 – 49616
    Helixi498 – 5003
    Beta strandi505 – 5128
    Helixi514 – 5218
    Helixi522 – 5243
    Beta strandi528 – 5325
    Beta strandi535 – 5417
    Beta strandi543 – 5519
    Beta strandi556 – 5594
    Beta strandi561 – 5644
    Beta strandi571 – 5733
    Beta strandi577 – 5804
    Helixi609 – 62315
    Beta strandi624 – 6285
    Helixi634 – 64714
    Beta strandi650 – 6556
    Helixi663 – 6708
    Helixi678 – 70427
    Turni705 – 7073
    Helixi717 – 72812
    Helixi730 – 7323
    Beta strandi733 – 7408
    Turni741 – 7444
    Beta strandi745 – 7484
    Beta strandi752 – 76817
    Helixi776 – 78510
    Helixi791 – 80313
    Beta strandi806 – 8083
    Helixi819 – 82911
    Beta strandi830 – 8334
    Beta strandi849 – 8524
    Helixi855 – 86410
    Helixi874 – 88916
    Beta strandi895 – 90612
    Beta strandi909 – 9135
    Beta strandi916 – 9216
    Helixi922 – 9265
    Beta strandi939 – 9457
    Beta strandi948 – 9536
    Helixi958 – 96811
    Turni973 – 9753
    Helixi976 – 98510
    Beta strandi988 – 9925
    Beta strandi995 – 9984
    Helixi1000 – 101112
    Helixi1015 – 10173
    Helixi1019 – 103416
    Helixi1039 – 105113

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1GKUX-ray2.70B33-1054[»]
    1GL9X-ray3.20B/C1-1054[»]
    ProteinModelPortaliO29238.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO29238.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini65 – 245181Helicase ATP-bindingUniRule annotationAdd
    BLAST
    Domaini506 – 662157ToprimUniRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni512 – 1054543Topoisomerase IAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi182 – 1854DEAD 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.

    Sequence similaritiesi

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

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri10 – 2718C4-type 1UniRule annotationAdd
    BLAST
    Zinc fingeri584 – 60118C4-type 2UniRule annotationAdd
    BLAST

    Keywords - Domaini

    Repeat, Zinc-finger

    Phylogenomic databases

    eggNOGiCOG1110.
    KOiK03170.
    OMAiTMRIAQD.

    Family and domain databases

    Gene3Di1.10.290.10. 1 hit.
    1.10.460.10. 2 hits.
    3.40.50.140. 1 hit.
    3.40.50.300. 3 hits.
    HAMAPiMF_01125. Reverse_gyrase.
    InterProiIPR011545. DNA/RNA_helicase_DEAD/DEAH_N.
    IPR014001. Helicase_ATP-bd.
    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.
    PF01131. Topoisom_bac. 1 hit.
    PF01751. Toprim. 1 hit.
    [Graphical view]
    PRINTSiPR00417. PRTPISMRASEI.
    SMARTiSM00487. DEXDc. 1 hit.
    SM00437. TOP1Ac. 1 hit.
    SM00436. TOP1Bc. 1 hit.
    SM00493. TOPRIM. 1 hit.
    [Graphical view]
    SUPFAMiSSF52540. SSF52540. 2 hits.
    SSF56712. SSF56712. 1 hit.
    TIGRFAMsiTIGR01054. rgy. 1 hit.
    PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
    PS50880. TOPRIM. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    O29238-1 [UniParc]FASTAAdd to Basket

    « Hide

    MIPVVYSNLC PVCGGDLESK EIEKHVCFRK KRSLCLFPED FLLKEFVEFF     50
    RKCVGEPRAI QKMWAKRILR KESFAATAPT GVGKTSFGLA MSLFLALKGK 100
    RCYVIFPTSL LVIQAAETIR KYAEKAGVGT ENLIGYYHGR IPKREKENFM 150
    QNLRNFKIVI TTTQFLSKHY RELGHFDFIF VDDVDAILKA SKNVDKLLHL 200
    LGFHYDLKTK SWVGEARGCL MVSTATAKKG KKAELFRQLL NFDIGSSRIT 250
    VRNVEDVAVN DESISTLSSI LEKLGTGGII YARTGEEAEE IYESLKNKFR 300
    IGIVTATKKG DYEKFVEGEI DHLIGTAHYY GTLVRGLDLP ERIRFAVFVG 350
    CPSFRVTIED IDSLSPQMVK LLAYLYRNVD EIERLLPAVE RHIDEVREIL 400
    KKVMGKERPQ AKDVVVREGE VIFPDLRTYI QGSGRTSRLF AGGLTKGASF 450
    LLEDDSELLS AFIERAKLYD IEFKSIDEVD FEKLSRELDE SRDRYRRRQE 500
    FDLIKPALFI VESPTKARQI SRFFGKPSVK VLDGAVVYEI PMQKYVLMVT 550
    ASIGHVVDLI TNRGFHGVLV NGRFVPVYAS IKRCRDCGYQ FTEDRESCPK 600
    CGSENVDNSR SRIEALRKLA HDAEFVIVGT DPDTEGEKIA WDLKNLLSGC 650
    GAVKRAEFHE VTRRAILEAL ESLRDVDENL VKAQVVRRIE DRWIGFVLSQ 700
    KLWERFNNRN LSAGRAQTPV LGWIIDRFQE SRERRKIAIV RDFDLVLEHD 750
    EEEFDLTIKL VEEREELRTP LPPYTTETML SDANRILKFS VKQTMQIAQE 800
    LFENGLITYH RTDSTRVSDV GQRIAKEYLG DDFVGREWGE SGAHECIRPT 850
    RPLTRDDVQR LIQEGVLVVE GLRWEHFALY DLIFRRFMAS QCRPFKVVVK 900
    KYSIEFDGKT AEEERIVRAE GRAYELYRAV WVKNELPTGT FRVKAEVKSV 950
    PKVLPFTQSE IIQMMKERGI GRPSTYATIV DRLFMRNYVV EKYGRMIPTK 1000
    LGIDVFRFLV RRYAKFVSED RTRDLESRMD AIERGELDYL KALEDLYAEI 1050
    KSID 1054
    Length:1,054
    Mass (Da):121,315
    Last modified:January 1, 1998 - v1
    Checksum:i551F19ADD62D7175
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE000782 Genomic DNA. Translation: AAB90219.1.
    PIRiH69377.
    RefSeqiNP_069857.1. NC_000917.1.
    WP_010878524.1. NC_000917.1.

    Genome annotation databases

    EnsemblBacteriaiAAB90219; AAB90219; AF_1024.
    GeneIDi1484247.
    KEGGiafu:AF1024.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE000782 Genomic DNA. Translation: AAB90219.1 .
    PIRi H69377.
    RefSeqi NP_069857.1. NC_000917.1.
    WP_010878524.1. NC_000917.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1GKU X-ray 2.70 B 33-1054 [» ]
    1GL9 X-ray 3.20 B/C 1-1054 [» ]
    ProteinModelPortali O29238.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 224325.AF1024.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAB90219 ; AAB90219 ; AF_1024 .
    GeneIDi 1484247.
    KEGGi afu:AF1024.

    Phylogenomic databases

    eggNOGi COG1110.
    KOi K03170.
    OMAi TMRIAQD.

    Enzyme and pathway databases

    BioCyci AFUL224325:GJBC-1046-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei O29238.

    Family and domain databases

    Gene3Di 1.10.290.10. 1 hit.
    1.10.460.10. 2 hits.
    3.40.50.140. 1 hit.
    3.40.50.300. 3 hits.
    HAMAPi MF_01125. Reverse_gyrase.
    InterProi IPR011545. DNA/RNA_helicase_DEAD/DEAH_N.
    IPR014001. Helicase_ATP-bd.
    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.
    PF01131. Topoisom_bac. 1 hit.
    PF01751. Toprim. 1 hit.
    [Graphical view ]
    PRINTSi PR00417. PRTPISMRASEI.
    SMARTi SM00487. DEXDc. 1 hit.
    SM00437. TOP1Ac. 1 hit.
    SM00436. TOP1Bc. 1 hit.
    SM00493. TOPRIM. 1 hit.
    [Graphical view ]
    SUPFAMi SSF52540. SSF52540. 2 hits.
    SSF56712. SSF56712. 1 hit.
    TIGRFAMsi TIGR01054. rgy. 1 hit.
    PROSITEi PS51192. HELICASE_ATP_BIND_1. 1 hit.
    PS50880. TOPRIM. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus."
      Klenk H.-P., Clayton R.A., Tomb J.-F., White O., Nelson K.E., Ketchum K.A., Dodson R.J., Gwinn M.L., Hickey E.K., Peterson J.D., Richardson D.L., Kerlavage A.R., Graham D.E., Kyrpides N.C., Fleischmann R.D., Quackenbush J., Lee N.H., Sutton G.G.
      , Gill S.R., Kirkness E.F., Dougherty B.A., McKenney K., Adams M.D., Loftus B.J., Peterson S.N., Reich C.I., McNeil L.K., Badger J.H., Glodek A., Zhou L., Overbeek R., Gocayne J.D., Weidman J.F., McDonald L.A., Utterback T.R., Cotton M.D., Spriggs T., Artiach P., Kaine B.P., Sykes S.M., Sadow P.W., D'Andrea K.P., Bowman C., Fujii C., Garland S.A., Mason T.M., Olsen G.J., Fraser C.M., Smith H.O., Woese C.R., Venter J.C.
      Nature 390:364-370(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126.
    2. "Studies of a positive supercoiling machine. Nucleotide hydrolysis and a multifunctional 'latch' in the mechanism of reverse gyrase."
      Rodriguez A.C.
      J. Biol. Chem. 277:29865-29873(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: N-TERMINAL DOMAIN FUNCTIONAL CHARACTERIZATION, MUTAGENESIS OF TYR-809.
    3. "Investigating the role of the latch in the positive supercoiling mechanism of reverse gyrase."
      Rodriguez A.C.
      Biochemistry 42:5993-6004(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: N-TERMINAL DOMAIN FUNCTIONAL CHARACTERIZATION.
    4. "Crystal structure of reverse gyrase: insights into the positive supercoiling of DNA."
      Rodriguez A.C., Stock D.
      EMBO J. 21:418-426(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 38-1054 AND IN COMPLEX WITH ADENYLYLIMIDODIPHOSPHATE (ADPNP).
      Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126.

    Entry informationi

    Entry nameiRGYR_ARCFU
    AccessioniPrimary (citable) accession number: O29238
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 16, 2004
    Last sequence update: January 1, 1998
    Last modified: October 1, 2014
    This is version 111 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

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3