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Protein

Ribose 1,5-bisphosphate isomerase

Gene

TK0185

Organism
Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the isomerization of ribose 1,5-bisphosphate (R15P) to ribulose 1,5-bisphosphate (RuBP), the CO2 acceptor and substrate for RubisCO. Only accepts the alpha-anomer of D-ribose 1,5-bisphosphate as substrate, being inactive on the beta-anomer. Displays a strict substrate specificity, since other phosphorylated sugars such as R5P, ribose, G16P, G6P, G1P, FBP, F6P,and PRPP, are not substrates. Functions in an archaeal AMP degradation pathway, together with AMP phosphorylase and RubisCO.3 Publications

Catalytic activityi

Alpha-D-ribose 1,5-bisphosphate = D-ribulose 1,5-bisphosphate.3 Publications

Enzyme regulationi

Is highly activated in the presence of AMP, with an increase of >40-fold in activity levels. Among other nucleotides, isomerase activity is slightly increased in the presence of GMP, but CMP, UMP, TMP, and NAD+ have no effect; therefore, AMP is likely the major activator of R15P isomerase in vivo. To a lesser extent, various compounds with an adenosyl moiety, such as dAMP, adenosine, or methylthioadenosine, can also act as activators. The regulation of this enzyme by AMP prevents excess degradation of intracellular AMP by the archaeal AMP degradation pathway.1 Publication

Kineticsi

kcat is 29.2 sec(-1) (in the presence of AMP, at 85 degrees Celsius).

  1. KM=0.6 mM for D-ribose 1,5-bisphosphate (in the presence of AMP, at 85 degrees Celsius)1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei63 – 631Substrate1 Publication
    Active sitei133 – 1331Proton acceptor1 Publication
    Active sitei202 – 2021Proton donor1 Publication
    Sitei227 – 2271Plays a key role in hexamerization
    Binding sitei238 – 2381Substrate1 Publication

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase

    Keywords - Biological processi

    Carbohydrate metabolism

    Enzyme and pathway databases

    BioCyciTKOD69014:GH72-187-MONOMER.
    BRENDAi5.3.1.29. 5246.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribose 1,5-bisphosphate isomerase (EC:5.3.1.29)
    Short name:
    R15P isomerase
    Short name:
    R15Pi
    Alternative name(s):
    Ribulose 1,5-bisphosphate synthase
    Short name:
    RuBP synthase
    Gene namesi
    Ordered Locus Names:TK0185
    OrganismiThermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
    Taxonomic identifieri69014 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
    Proteomesi
    • UP000000536 Componenti: Chromosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi133 – 1331C → A or S: Loss of catalytic activity. 1 Publication
    Mutagenesisi202 – 2021D → N: Loss of catalytic activity. 1 Publication
    Mutagenesisi227 – 2271R → E: Impairs molecular assembly. 60-fold decrease in catalytic activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 322322Ribose 1,5-bisphosphate isomerasePRO_0000422826Add
    BLAST

    Expressioni

    Inductioni

    Up-regulated by nucleosides (at protein level).1 Publication

    Interactioni

    Subunit structurei

    Homohexamer; trimer of dimers.1 Publication

    Protein-protein interaction databases

    STRINGi69014.TK0185.

    Structurei

    Secondary structure

    1
    322
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi6 – 1510Combined sources
    Helixi22 – 3918Combined sources
    Helixi45 – 6016Combined sources
    Helixi68 – 8518Combined sources
    Helixi90 – 12031Combined sources
    Beta strandi128 – 1314Combined sources
    Helixi136 – 14712Combined sources
    Beta strandi153 – 1575Combined sources
    Turni160 – 1634Combined sources
    Helixi164 – 17411Combined sources
    Beta strandi179 – 1824Combined sources
    Helixi184 – 1863Combined sources
    Turni187 – 1904Combined sources
    Helixi191 – 1933Combined sources
    Beta strandi195 – 1995Combined sources
    Beta strandi202 – 2043Combined sources
    Beta strandi210 – 2134Combined sources
    Helixi216 – 22510Combined sources
    Beta strandi229 – 2335Combined sources
    Helixi236 – 2383Combined sources
    Beta strandi244 – 2474Combined sources
    Helixi256 – 2583Combined sources
    Helixi262 – 2654Combined sources
    Beta strandi272 – 2743Combined sources
    Beta strandi277 – 2826Combined sources
    Helixi284 – 2863Combined sources
    Beta strandi288 – 2925Combined sources
    Beta strandi295 – 2973Combined sources
    Helixi299 – 3013Combined sources
    Helixi302 – 3109Combined sources
    Beta strandi314 – 3163Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3A11X-ray2.50A/B/C/D/E/F1-322[»]
    3A9CX-ray2.60A/B/C/D/E/F1-322[»]
    3VM6X-ray2.85A/B/C1-322[»]
    ProteinModelPortaliQ5JFM9.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ5JFM9.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni20 – 234Substrate binding
    Regioni135 – 1373Substrate binding
    Regioni212 – 2132Substrate binding

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiarCOG01124. Archaea.
    COG1184. LUCA.
    HOGENOMiHOG000224731.
    InParanoidiQ5JFM9.
    KOiK18237.
    OMAiEEFGWAL.

    Family and domain databases

    Gene3Di1.20.120.420. 1 hit.
    InterProiIPR000649. IF-2B-related.
    IPR011559. Initiation_fac_2B_a/b/d.
    IPR027363. M1Pi_N.
    IPR005250. Ribulose_e2b2.
    [Graphical view]
    PfamiPF01008. IF-2B. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR00524. eIF-2B_rel. 1 hit.
    TIGR00511. ribulose_e2b2. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q5JFM9-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAVVKEVLEI AEKIKNMEIR GAGKIARSAA YALQLQAEKS KATNVDEFWK
    60 70 80 90 100
    EMKQAAKILF ETRPTAVSLP NALRYVMHRG KIAYSSGADL EQLRFVIINA
    110 120 130 140 150
    AKEFIHNSEK ALERIGEFGA KRIEDGDVIM THCHSKAAIS VMKTAWEQGK
    160 170 180 190 200
    DIKVIVTETR PKWQGKITAK ELASYGIPVI YVVDSAARHY MKMTDKVVMG
    210 220 230 240 250
    ADSITVNGAV INKIGTALIA LTAKEHRVWT MIAAETYKFH PETMLGQLVE
    260 270 280 290 300
    IEMRDPTEVI PEDELKTWPK NIEVWNPAFD VTPPEYVDVI ITERGIIPPY
    310 320
    AAIDILREEF GWALKYTEPW ED
    Length:322
    Mass (Da):36,302
    Last modified:February 15, 2005 - v1
    Checksum:i44A19FD24E140250
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AP006878 Genomic DNA. Translation: BAD84374.1.
    RefSeqiWP_011249140.1. NC_006624.1.

    Genome annotation databases

    EnsemblBacteriaiBAD84374; BAD84374; TK0185.
    GeneIDi3235541.
    KEGGitko:TK0185.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AP006878 Genomic DNA. Translation: BAD84374.1.
    RefSeqiWP_011249140.1. NC_006624.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3A11X-ray2.50A/B/C/D/E/F1-322[»]
    3A9CX-ray2.60A/B/C/D/E/F1-322[»]
    3VM6X-ray2.85A/B/C1-322[»]
    ProteinModelPortaliQ5JFM9.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi69014.TK0185.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiBAD84374; BAD84374; TK0185.
    GeneIDi3235541.
    KEGGitko:TK0185.

    Phylogenomic databases

    eggNOGiarCOG01124. Archaea.
    COG1184. LUCA.
    HOGENOMiHOG000224731.
    InParanoidiQ5JFM9.
    KOiK18237.
    OMAiEEFGWAL.

    Enzyme and pathway databases

    BioCyciTKOD69014:GH72-187-MONOMER.
    BRENDAi5.3.1.29. 5246.

    Miscellaneous databases

    EvolutionaryTraceiQ5JFM9.

    Family and domain databases

    Gene3Di1.20.120.420. 1 hit.
    InterProiIPR000649. IF-2B-related.
    IPR011559. Initiation_fac_2B_a/b/d.
    IPR027363. M1Pi_N.
    IPR005250. Ribulose_e2b2.
    [Graphical view]
    PfamiPF01008. IF-2B. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR00524. eIF-2B_rel. 1 hit.
    TIGR00511. ribulose_e2b2. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiR15PI_THEKO
    AccessioniPrimary (citable) accession number: Q5JFM9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 26, 2013
    Last sequence update: February 15, 2005
    Last modified: September 7, 2016
    This is version 78 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Reaction proceeds via a cis-phosphoenolate intermediate.

    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

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.