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Protein

AMP phosphorylase

Gene

deoA

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.2 Publications
CMP + phosphate = cytosine + alpha-D-ribose 1,5-bisphosphate.1 Publication
UMP + phosphate = uracil + alpha-D-ribose 1,5-bisphosphate.1 Publication

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 Publication

Manual assertion based on experiment ini

  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)DescriptionActionsGraphical viewLength
    Binding sitei168AMP; via amide nitrogen1 Publication1
    Binding sitei203AMP; via amide nitrogen1 Publication1
    Active sitei256Proton donor1 Publication1
    Binding sitei264AMP1 Publication1
    Binding sitei288AMP1 Publication1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi194 – 199AMP1 Publication6

    GO - Molecular functioni

    • AMP binding Source: UniProtKB
    • phosphate ion binding Source: UniProtKB
    • phosphorylase activity Source: GO_Central
    • 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:GH72-359-MONOMER.
    BRENDAi2.4.2.B11. 5246.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    AMP phosphorylaseUniRule annotation (EC:2.4.2.57UniRule annotation2 Publications)
    Short name:
    AMPpaseUniRule annotation
    Alternative name(s):
    Nucleoside monophosphate phosphorylaseUniRule annotation
    Short name:
    NMP phosphorylaseUniRule annotation
    Gene namesi
    Name:deoA1 Publication
    Ordered Locus Names:TK0352
    OrganismiThermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
    Taxonomic identifieri69014 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
    Proteomesi
    • UP000000536 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi256D → N or A: Almost complete loss of activity. 1 Publication1
    Mutagenesisi288K → A: Almost complete loss of activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000590931 – 503AMP phosphorylaseAdd BLAST503

    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

    1503
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi2 – 8Combined sources7
    Beta strandi16 – 19Combined sources4
    Helixi21 – 27Combined sources7
    Beta strandi34 – 41Combined sources8
    Beta strandi43 – 51Combined sources9
    Beta strandi58 – 62Combined sources5
    Helixi63 – 66Combined sources4
    Beta strandi76 – 81Combined sources6
    Helixi87 – 95Combined sources9
    Helixi102 – 113Combined sources12
    Helixi119 – 132Combined sources14
    Helixi136 – 148Combined sources13
    Beta strandi159 – 165Combined sources7
    Helixi174 – 184Combined sources11
    Beta strandi188 – 193Combined sources6
    Beta strandi197 – 200Combined sources4
    Helixi203 – 207Combined sources5
    Turni208 – 210Combined sources3
    Helixi217 – 227Combined sources11
    Beta strandi228 – 234Combined sources7
    Beta strandi237 – 240Combined sources4
    Helixi241 – 253Combined sources13
    Helixi258 – 272Combined sources15
    Beta strandi276 – 284Combined sources9
    Beta strandi287 – 289Combined sources3
    Helixi292 – 308Combined sources17
    Beta strandi312 – 319Combined sources8
    Beta strandi327 – 329Combined sources3
    Helixi330 – 343Combined sources14
    Helixi348 – 364Combined sources17
    Helixi373 – 382Combined sources10
    Helixi385 – 396Combined sources12
    Helixi405 – 407Combined sources3
    Beta strandi412 – 418Combined sources7
    Beta strandi420 – 428Combined sources9
    Helixi430 – 439Combined sources10
    Turni440 – 444Combined sources5
    Beta strandi445 – 447Combined sources3
    Beta strandi449 – 452Combined sources4
    Beta strandi465 – 473Combined sources9
    Helixi474 – 487Combined sources14
    Beta strandi490 – 493Combined sources4

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    SMRiQ5JCX3.
    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

    Belongs to the thymidine/pyrimidine-nucleoside phosphorylase family. Type 2 subfamily.UniRule annotation

    Phylogenomic databases

    eggNOGiarCOG02013. Archaea.
    COG0213. LUCA.
    HOGENOMiHOG000252767.
    InParanoidiQ5JCX3.
    KOiK18931.
    OMAiYVEVAIT.

    Family and domain databases

    Gene3Di3.40.1030.10. 1 hit.
    3.90.1170.30. 1 hit.
    HAMAPiMF_02132. AMP_phosphorylase. 1 hit.
    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.

    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.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    SMRiQ5JCX3.
    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

    eggNOGiarCOG02013. Archaea.
    COG0213. LUCA.
    HOGENOMiHOG000252767.
    InParanoidiQ5JCX3.
    KOiK18931.
    OMAiYVEVAIT.

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-13274.
    TKOD69014:GH72-359-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. 1 hit.
    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...

    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: November 2, 2016
    This is version 87 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

    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.