Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Basket 0
(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

Q5JCX3

- AMPPA_THEKO

UniProt

Q5JCX3 - AMPPA_THEKO

Protein

AMP phosphorylase

Gene

TK0352

Organism
Thermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
    • BLAST
    • Align
    • Format
    • Add to basket
    • History
      Entry version 75 (01 Oct 2014)
      Sequence version 1 (15 Feb 2005)
      Previous versions | rss
    • Help video
    • Feedback
    • Comment

    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

    1. AMP binding Source: UniProtKB
    2. phosphate ion binding Source: UniProtKB
    3. phosphorylase activity Source: InterPro
    4. thymidine phosphorylase activity Source: InterPro
    5. transferase activity, transferring pentosyl groups Source: UniProtKB

    GO - Biological processi

    1. AMP catabolic process Source: UniProtKB
    2. pyrimidine deoxyribonucleoside metabolic process Source: InterPro
    3. pyrimidine nucleobase metabolic process Source: InterPro

    Keywords - Molecular functioni

    Glycosyltransferase, Transferase

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-13274.
    TKOD69014:GH72-358-MONOMER.

    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 kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
    Taxonomic identifieri69014 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
    ProteomesiUP000000536: 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 – 87
    Beta strandi16 – 194
    Helixi21 – 277
    Beta strandi34 – 418
    Beta strandi43 – 519
    Beta strandi58 – 625
    Helixi63 – 664
    Beta strandi76 – 816
    Helixi87 – 959
    Helixi102 – 11312
    Helixi119 – 13214
    Helixi136 – 14813
    Beta strandi159 – 1657
    Helixi174 – 18411
    Beta strandi188 – 1936
    Beta strandi197 – 2004
    Helixi203 – 2075
    Turni208 – 2103
    Helixi217 – 22711
    Beta strandi228 – 2347
    Beta strandi237 – 2404
    Helixi241 – 25313
    Helixi258 – 27215
    Beta strandi276 – 2849
    Beta strandi287 – 2893
    Helixi292 – 30817
    Beta strandi312 – 3198
    Beta strandi327 – 3293
    Helixi330 – 34314
    Helixi348 – 36417
    Helixi373 – 38210
    Helixi385 – 39612
    Helixi405 – 4073
    Beta strandi412 – 4187
    Beta strandi420 – 4289
    Helixi430 – 43910
    Turni440 – 4445
    Beta strandi445 – 4473
    Beta strandi449 – 4524
    Beta strandi465 – 4739
    Helixi474 – 48714
    Beta strandi490 – 4934

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    KOiK00758.
    OMAiLEWAFDE.

    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.
    IPR000053. Pyrmidine_PPase.
    IPR017872. Pyrmidine_PPase_CS.
    IPR013466. Thymidine/AMP_Pase.
    [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

    MKAKIRILDM FSGRYTVLIN EEDAKEAKLH PDDLVKIEAG KKAVYGSVAL    50
    SNLVGKGEVG ISRDVLDLHN FSEGETVSVI PAGTPESVRY IKKKMHGEKL 100
    RKVEIEAIVR DIVDRKLRDI EISSFVTALE INGLDMDEIA ALTIAMAETG 150
    DMLDIDRKPI MDVHSIGGVP GNKTNILVVP IVAAAGLTIP KTSSRAITSA 200
    AGTADVVEVF ADVSFSLDEI KRIVEKVGAC LVWGGALNLA PADDITIKAE 250
    RALSIDPTGL MLASIMSKKY AMGSQYVLID IPTGKGVKVE TVEEARSLAR 300
    DFIELGKRLG QYVEVAITYG GQPIGHTVGP ALEAREALSA LMTGKGPGSL 350
    IEKATGLAGI LLEMGGVAPA GTGKKMAKEI LESGKAWEKM KEIIEAQGGD 400
    PNIKPEEIPI GDKTYTFTAA TSGYVTAIDN RAITAIARAA GAPEDKGAGI 450
    ELYVKVGEKV KEGDPLFTIH AEHEARLDQA IVLARRTEPI RIEGMVLQRI 500
    GNI 503
    Length:503
    Mass (Da):53,651
    Last modified:February 15, 2005 - v1
    Checksum:i63AB57AE279ACCBA
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP006878 Genomic DNA. Translation: BAD84541.1.
    RefSeqiYP_182765.1. NC_006624.1.

    Genome annotation databases

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

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP006878 Genomic DNA. Translation: BAD84541.1 .
    RefSeqi YP_182765.1. NC_006624.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4GA4 X-ray 3.51 A/B 85-503 [» ]
    4GA5 X-ray 3.25 A/B/C/D/E/F/G/H 1-493 [» ]
    4GA6 X-ray 2.21 A/B 1-493 [» ]
    ProteinModelPortali Q5JCX3.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 69014.TK0352.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAD84541 ; BAD84541 ; TK0352 .
    GeneIDi 3235858.
    KEGGi tko:TK0352.

    Phylogenomic databases

    eggNOGi COG0213.
    HOGENOMi HOG000252767.
    KOi K00758.
    OMAi LEWAFDE.

    Enzyme and pathway databases

    BioCyci MetaCyc:MONOMER-13274.
    TKOD69014:GH72-358-MONOMER.

    Family and domain databases

    Gene3Di 3.40.1030.10. 1 hit.
    3.90.1170.30. 1 hit.
    HAMAPi MF_02132. AMP_phosphorylase.
    InterProi IPR017713. AMP_phosphorylase.
    IPR000312. Glycosyl_Trfase_fam3.
    IPR017459. Glycosyl_Trfase_fam3_N_dom.
    IPR013102. PYNP_C.
    IPR000053. Pyrmidine_PPase.
    IPR017872. Pyrmidine_PPase_CS.
    IPR013466. Thymidine/AMP_Pase.
    [Graphical view ]
    PANTHERi PTHR10515. PTHR10515. 1 hit.
    Pfami PF02885. Glycos_trans_3N. 1 hit.
    PF00591. Glycos_transf_3. 1 hit.
    PF07831. PYNP_C. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF000478. TP_PyNP. 1 hit.
    SMARTi SM00941. PYNP_C. 1 hit.
    [Graphical view ]
    SUPFAMi SSF47648. SSF47648. 1 hit.
    SSF52418. SSF52418. 1 hit.
    SSF54680. SSF54680. 1 hit.
    TIGRFAMsi TIGR03327. AMP_phos. 1 hit.
    TIGR02645. ARCH_P_rylase. 1 hit.
    PROSITEi PS00647. THYMID_PHOSPHORYLASE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 75 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