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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: -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
  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

    Keywordsi

    Molecular functionAllosteric enzyme, Glycosyltransferase, Transferase

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-13274
    TKOD69014:G1G2A-349-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

    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

    Proteomic databases

    PRIDEiQ5JCX3

    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
    OMAiVHSIGGV
    OrthoDBiPOG093Z01M3

    Family and domain databases

    Gene3Di3.40.1030.10, 1 hit
    3.90.1170.30, 1 hit
    HAMAPiMF_02132 AMP_phosphorylase, 1 hit
    InterProiView protein in InterPro
    IPR017713 AMP_phosphorylase
    IPR000312 Glycosyl_Trfase_fam3
    IPR017459 Glycosyl_Trfase_fam3_N_dom
    IPR036320 Glycosyl_Trfase_fam3_N_dom)sf
    IPR035902 Nuc_phospho_transferase
    IPR036566 PYNP-like_C_sf
    IPR013102 PYNP_C
    IPR017872 Pyrmidine_PPase_CS
    IPR013466 Thymidine/AMP_Pase
    IPR000053 Thymidine/pyrmidine_PPase
    PANTHERiPTHR10515 PTHR10515, 1 hit
    PfamiView protein in Pfam
    PF02885 Glycos_trans_3N, 1 hit
    PF00591 Glycos_transf_3, 1 hit
    PF07831 PYNP_C, 1 hit
    PIRSFiPIRSF000478 TP_PyNP, 1 hit
    SMARTiView protein in SMART
    SM00941 PYNP_C, 1 hit
    SUPFAMiSSF47648 SSF47648, 1 hit
    SSF52418 SSF52418, 1 hit
    SSF54680 SSF54680, 1 hit
    TIGRFAMsiTIGR03327 AMP_phos, 1 hit
    TIGR02645 ARCH_P_rylase, 1 hit
    PROSITEiView protein in PROSITE
    PS00647 THYMID_PHOSPHORYLASE, 1 hit

    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
    PATRICifig|69014.16.peg.349

    Similar proteinsi

    Entry informationi

    Entry nameiAMPPA_THEKO
    AccessioniPrimary (citable) accession number: Q5JCX3
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 30, 2005
    Last sequence update: February 15, 2005
    Last modified: May 23, 2018
    This is version 96 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    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

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