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Protein

AMP phosphorylase

Gene

TK0352

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 conversion of AMP and phosphate to adenine and ribose 1,5-bisphosphate (R15P). Exhibits phosphorylase activity toward CMP, dCMP and UMP in addition to AMP. Functions in an archaeal AMP degradation pathway, together with R15P isomerase and RubisCO.2 Publications

Catalytic activityi

AMP + phosphate = adenine + alpha-D-ribose 1,5-bisphosphate.
CMP + phosphate = cytosine + alpha-D-ribose 1,5-bisphosphate.
UMP + phosphate = uracil + alpha-D-ribose 1,5-bisphosphate.

Enzyme regulationi

AMP phosphorolysis is allosterically regulated by the substrate AMP.1 Publication

Kineticsi

kcat is 39.1 sec(-1), 15.0 sec(-1), 10.5 sec(-1) and 2.7 sec(-1), with CMP, AMP, UMP, and GMP as substrate, respectively (at 85 degrees Celsius). KM for AMP was not determined because the reaction does not follow Michaelis-Menten kinetics.

  1. KM=6.2 mM for CMP (in the presence of AMP, at 85 degrees Celsius)1 Publication
  2. KM=4.4 mM for UMP (in the presence of AMP, at 85 degrees Celsius)1 Publication
  3. KM=18.5 mM for GMP (in the presence of AMP, at 85 degrees Celsius)1 Publication
  4. KM=2.8 mM for phosphate (in the presence of AMP, at 85 degrees Celsius)1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei168 – 1681AMP; via amide nitrogen
    Binding sitei203 – 2031AMP; via amide nitrogen
    Active sitei256 – 2561Proton donor1 Publication
    Binding sitei264 – 2641AMP
    Binding sitei288 – 2881AMP

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi194 – 1996AMP

    GO - Molecular functioni

    • AMP binding Source: UniProtKB
    • phosphate ion binding Source: UniProtKB
    • phosphorylase activity Source: InterPro
    • thymidine phosphorylase activity Source: InterPro
    • transferase activity, transferring pentosyl groups Source: UniProtKB

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Glycosyltransferase, Transferase

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-13274.
    TKOD69014:GH72-358-MONOMER.
    BRENDAi2.4.2.B11. 5246.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    AMP phosphorylase (EC:2.4.2.57)
    Short name:
    AMPpase
    Alternative name(s):
    Nucleoside monophosphate phosphorylase
    Short name:
    NMP phosphorylase
    Gene namesi
    Ordered Locus Names:TK0352
    OrganismiThermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
    Taxonomic identifieri69014 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
    ProteomesiUP000000536 Componenti: Chromosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi256 – 2561D → N or A: Almost complete loss of activity. 1 Publication
    Mutagenesisi288 – 2881K → A: Almost complete loss of activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 503503AMP phosphorylasePRO_0000059093Add
    BLAST

    Expressioni

    Inductioni

    Constitutively expressed (at protein level). Does not respond to the addition of nucleosides.1 Publication

    Interactioni

    Subunit structurei

    Forms an exceptionally large macromolecular structure (>40-mers) in solution.1 Publication

    Protein-protein interaction databases

    STRINGi69014.TK0352.

    Structurei

    Secondary structure

    1
    503
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 87Combined sources
    Beta strandi16 – 194Combined sources
    Helixi21 – 277Combined sources
    Beta strandi34 – 418Combined sources
    Beta strandi43 – 519Combined sources
    Beta strandi58 – 625Combined sources
    Helixi63 – 664Combined sources
    Beta strandi76 – 816Combined sources
    Helixi87 – 959Combined sources
    Helixi102 – 11312Combined sources
    Helixi119 – 13214Combined sources
    Helixi136 – 14813Combined sources
    Beta strandi159 – 1657Combined sources
    Helixi174 – 18411Combined sources
    Beta strandi188 – 1936Combined sources
    Beta strandi197 – 2004Combined sources
    Helixi203 – 2075Combined sources
    Turni208 – 2103Combined sources
    Helixi217 – 22711Combined sources
    Beta strandi228 – 2347Combined sources
    Beta strandi237 – 2404Combined sources
    Helixi241 – 25313Combined sources
    Helixi258 – 27215Combined sources
    Beta strandi276 – 2849Combined sources
    Beta strandi287 – 2893Combined sources
    Helixi292 – 30817Combined sources
    Beta strandi312 – 3198Combined sources
    Beta strandi327 – 3293Combined sources
    Helixi330 – 34314Combined sources
    Helixi348 – 36417Combined sources
    Helixi373 – 38210Combined sources
    Helixi385 – 39612Combined sources
    Helixi405 – 4073Combined sources
    Beta strandi412 – 4187Combined sources
    Beta strandi420 – 4289Combined sources
    Helixi430 – 43910Combined sources
    Turni440 – 4445Combined sources
    Beta strandi445 – 4473Combined sources
    Beta strandi449 – 4524Combined sources
    Beta strandi465 – 4739Combined sources
    Helixi474 – 48714Combined sources
    Beta strandi490 – 4934Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4GA4X-ray3.51A/B85-503[»]
    4GA5X-ray3.25A/B/C/D/E/F/G/H1-493[»]
    4GA6X-ray2.21A/B1-493[»]
    ProteinModelPortaliQ5JCX3.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domaini

    The N-terminal domain (residues 1-84), characteristic of archaeal AMPpases, is essential for enzymatic activity, participating in multimerization as well as domain closure of the active site upon substrate binding. Harbors two dimer interfaces within a single molecule: one by the central domain and the other by the C-terminal domain; these two interactions can continuously occur in a repetitive manner, leading to multimerization.1 Publication

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0213.
    HOGENOMiHOG000252767.
    InParanoidiQ5JCX3.
    KOiK18931.
    OMAiESVPGFH.

    Family and domain databases

    Gene3Di3.40.1030.10. 1 hit.
    3.90.1170.30. 1 hit.
    HAMAPiMF_02132. AMP_phosphorylase.
    InterProiIPR017713. AMP_phosphorylase.
    IPR000312. Glycosyl_Trfase_fam3.
    IPR017459. Glycosyl_Trfase_fam3_N_dom.
    IPR013102. PYNP_C.
    IPR017872. Pyrmidine_PPase_CS.
    IPR013466. Thymidine/AMP_Pase.
    IPR000053. Thymidine/pyrmidine_PPase.
    [Graphical view]
    PANTHERiPTHR10515. PTHR10515. 1 hit.
    PfamiPF02885. Glycos_trans_3N. 1 hit.
    PF00591. Glycos_transf_3. 1 hit.
    PF07831. PYNP_C. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000478. TP_PyNP. 1 hit.
    SMARTiSM00941. PYNP_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF47648. SSF47648. 1 hit.
    SSF52418. SSF52418. 1 hit.
    SSF54680. SSF54680. 1 hit.
    TIGRFAMsiTIGR03327. AMP_phos. 1 hit.
    TIGR02645. ARCH_P_rylase. 1 hit.
    PROSITEiPS00647. THYMID_PHOSPHORYLASE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q5JCX3-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKAKIRILDM FSGRYTVLIN EEDAKEAKLH PDDLVKIEAG KKAVYGSVAL
    60 70 80 90 100
    SNLVGKGEVG ISRDVLDLHN FSEGETVSVI PAGTPESVRY IKKKMHGEKL
    110 120 130 140 150
    RKVEIEAIVR DIVDRKLRDI EISSFVTALE INGLDMDEIA ALTIAMAETG
    160 170 180 190 200
    DMLDIDRKPI MDVHSIGGVP GNKTNILVVP IVAAAGLTIP KTSSRAITSA
    210 220 230 240 250
    AGTADVVEVF ADVSFSLDEI KRIVEKVGAC LVWGGALNLA PADDITIKAE
    260 270 280 290 300
    RALSIDPTGL MLASIMSKKY AMGSQYVLID IPTGKGVKVE TVEEARSLAR
    310 320 330 340 350
    DFIELGKRLG QYVEVAITYG GQPIGHTVGP ALEAREALSA LMTGKGPGSL
    360 370 380 390 400
    IEKATGLAGI LLEMGGVAPA GTGKKMAKEI LESGKAWEKM KEIIEAQGGD
    410 420 430 440 450
    PNIKPEEIPI GDKTYTFTAA TSGYVTAIDN RAITAIARAA GAPEDKGAGI
    460 470 480 490 500
    ELYVKVGEKV KEGDPLFTIH AEHEARLDQA IVLARRTEPI RIEGMVLQRI

    GNI
    Length:503
    Mass (Da):53,651
    Last modified:February 15, 2005 - v1
    Checksum:i63AB57AE279ACCBA
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AP006878 Genomic DNA. Translation: BAD84541.1.
    RefSeqiWP_011249307.1. NC_006624.1.
    YP_182765.1. NC_006624.1.

    Genome annotation databases

    EnsemblBacteriaiBAD84541; BAD84541; TK0352.
    GeneIDi3235858.
    KEGGitko:TK0352.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AP006878 Genomic DNA. Translation: BAD84541.1.
    RefSeqiWP_011249307.1. NC_006624.1.
    YP_182765.1. NC_006624.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4GA4X-ray3.51A/B85-503[»]
    4GA5X-ray3.25A/B/C/D/E/F/G/H1-493[»]
    4GA6X-ray2.21A/B1-493[»]
    ProteinModelPortaliQ5JCX3.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi69014.TK0352.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiBAD84541; BAD84541; TK0352.
    GeneIDi3235858.
    KEGGitko:TK0352.

    Phylogenomic databases

    eggNOGiCOG0213.
    HOGENOMiHOG000252767.
    InParanoidiQ5JCX3.
    KOiK18931.
    OMAiESVPGFH.

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-13274.
    TKOD69014:GH72-358-MONOMER.
    BRENDAi2.4.2.B11. 5246.

    Family and domain databases

    Gene3Di3.40.1030.10. 1 hit.
    3.90.1170.30. 1 hit.
    HAMAPiMF_02132. AMP_phosphorylase.
    InterProiIPR017713. AMP_phosphorylase.
    IPR000312. Glycosyl_Trfase_fam3.
    IPR017459. Glycosyl_Trfase_fam3_N_dom.
    IPR013102. PYNP_C.
    IPR017872. Pyrmidine_PPase_CS.
    IPR013466. Thymidine/AMP_Pase.
    IPR000053. Thymidine/pyrmidine_PPase.
    [Graphical view]
    PANTHERiPTHR10515. PTHR10515. 1 hit.
    PfamiPF02885. Glycos_trans_3N. 1 hit.
    PF00591. Glycos_transf_3. 1 hit.
    PF07831. PYNP_C. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000478. TP_PyNP. 1 hit.
    SMARTiSM00941. PYNP_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF47648. SSF47648. 1 hit.
    SSF52418. SSF52418. 1 hit.
    SSF54680. SSF54680. 1 hit.
    TIGRFAMsiTIGR03327. AMP_phos. 1 hit.
    TIGR02645. ARCH_P_rylase. 1 hit.
    PROSITEiPS00647. THYMID_PHOSPHORYLASE. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "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.
    2. "Archaeal type III RuBisCOs function in a pathway for AMP metabolism."
      Sato T., Atomi H., Imanaka T.
      Science 315:1003-1006(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, PATHWAY.
      Strain: ATCC BAA-918 / JCM 12380 / KOD1.
    3. "Enzymatic characterization of AMP phosphorylase and ribose-1,5-bisphosphate isomerase functioning in an archaeal AMP metabolic pathway."
      Aono R., Sato T., Yano A., Yoshida S., Nishitani Y., Miki K., Imanaka T., Atomi H.
      J. Bacteriol. 194:6847-6855(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, ENZYME REGULATION, KINETIC PARAMETERS, INDUCTION, PATHWAY.
      Strain: ATCC BAA-918 / JCM 12380 / KOD1.
    4. "Structure analysis of archaeal AMP phosphorylase reveals two unique modes of dimerization."
      Nishitani Y., Aono R., Nakamura A., Sato T., Atomi H., Imanaka T., Miki K.
      J. Mol. Biol. 425:2709-2721(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.21 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH SUBSTRATE, SUBUNIT, DOMAIN, ACTIVE SITE, MUTAGENESIS OF ASP-256 AND LYS-288.
      Strain: ATCC BAA-918 / JCM 12380 / KOD1.

    Entry informationi

    Entry nameiAMPPA_THEKO
    AccessioniPrimary (citable) accession number: Q5JCX3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 30, 2005
    Last sequence update: February 15, 2005
    Last modified: June 24, 2015
    This is version 81 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Allosteric enzyme, 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

    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 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.