Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
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)DescriptionActionsGraphical viewLength
    Binding sitei63Substrate1 Publication1
    Active sitei133Proton acceptor1 Publication1
    Active sitei202Proton donor1 Publication1
    Sitei227Plays a key role in hexamerization1
    Binding sitei238Substrate1 Publication1

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase

    Keywords - Biological processi

    Carbohydrate metabolism

    Enzyme and pathway databases

    BioCyciTKOD69014:GH72-188-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)DescriptionActionsGraphical viewLength
    Mutagenesisi133C → A or S: Loss of catalytic activity. 1 Publication1
    Mutagenesisi202D → N: Loss of catalytic activity. 1 Publication1
    Mutagenesisi227R → E: Impairs molecular assembly. 60-fold decrease in catalytic activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00004228261 – 322Ribose 1,5-bisphosphate isomeraseAdd BLAST322

    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

    1322
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi6 – 15Combined sources10
    Helixi22 – 39Combined sources18
    Helixi45 – 60Combined sources16
    Helixi68 – 85Combined sources18
    Helixi90 – 120Combined sources31
    Beta strandi128 – 131Combined sources4
    Helixi136 – 147Combined sources12
    Beta strandi153 – 157Combined sources5
    Turni160 – 163Combined sources4
    Helixi164 – 174Combined sources11
    Beta strandi179 – 182Combined sources4
    Helixi184 – 186Combined sources3
    Turni187 – 190Combined sources4
    Helixi191 – 193Combined sources3
    Beta strandi195 – 199Combined sources5
    Beta strandi202 – 204Combined sources3
    Beta strandi210 – 213Combined sources4
    Helixi216 – 225Combined sources10
    Beta strandi229 – 233Combined sources5
    Helixi236 – 238Combined sources3
    Beta strandi244 – 247Combined sources4
    Helixi256 – 258Combined sources3
    Helixi262 – 265Combined sources4
    Beta strandi272 – 274Combined sources3
    Beta strandi277 – 282Combined sources6
    Helixi284 – 286Combined sources3
    Beta strandi288 – 292Combined sources5
    Beta strandi295 – 297Combined sources3
    Helixi299 – 301Combined sources3
    Helixi302 – 310Combined sources9
    Beta strandi314 – 316Combined sources3

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    SMRiQ5JFM9.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ5JFM9.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni20 – 23Substrate binding4
    Regioni135 – 137Substrate binding3
    Regioni212 – 213Substrate binding2

    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
    PDB 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.
    SMRiQ5JFM9.
    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:GH72-188-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: November 2, 2016
    This is version 79 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.