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Protein

UMP-CMP kinase

Gene

pyrK

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the phosphorylation of pyrimidine nucleoside monophosphates at the expense of ATP. Plays an important role in de novo pyrimidine nucleotide biosynthesis. Has preference for UMP and CMP as phosphate acceptors.

Catalytic activityi

ATP + (d)CMP = ADP + (d)CDP.UniRule annotation1 Publication
ATP + UMP = ADP + UDP.UniRule annotation1 Publication

Cofactori

Mg2+UniRule annotation1 PublicationNote: Binds 1 Mg(2+) ion per monomer. The Mg2+ ion binds to water and substrates.UniRule annotation1 Publication

Kineticsi

  1. KM=25 µM for ATP1 Publication
  2. KM=0.4 mM for UMP1 Publication
  3. KM=0.1 mM for CMP1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei43 – 431NMP
    Binding sitei98 – 981CMPUniRule annotation2 Publications
    Binding sitei132 – 1321ATP
    Binding sitei138 – 1381NMP
    Binding sitei149 – 1491NMP
    Binding sitei177 – 1771ATP; via carbonyl oxygen

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi17 – 226ATP
    Nucleotide bindingi64 – 663NMP
    Nucleotide bindingi91 – 944NMP

    GO - Molecular functioni

    • ATP binding Source: dictyBase
    • cytidylate kinase activity Source: dictyBase
    • magnesium ion binding Source: dictyBase
    • phosphotransferase activity, phosphate group as acceptor Source: dictyBase
    • UMP kinase activity Source: dictyBase

    GO - Biological processi

    • 'de novo' pyrimidine nucleobase biosynthetic process Source: InterPro
    • CDP biosynthetic process Source: dictyBase
    • nucleotide phosphorylation Source: GOC
    • nucleotide salvage Source: dictyBase
    • pyrimidine nucleobase salvage Source: dictyBase
    • UDP biosynthetic process Source: dictyBase
    Complete GO annotation...

    Keywords - Molecular functioni

    Kinase, Transferase

    Keywords - Biological processi

    Pyrimidine biosynthesis

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BRENDAi2.7.4.14. 1939.
    ReactomeiREACT_339252. Synthesis and interconversion of nucleotide di- and triphosphates.
    SABIO-RKP20425.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    UMP-CMP kinaseUniRule annotation (EC:2.7.4.14UniRule annotation)
    Alternative name(s):
    Deoxycytidylate kinaseUniRule annotation
    Short name:
    CKUniRule annotation
    Short name:
    dCMP kinaseUniRule annotation
    Uridine monophosphate/cytidine monophosphate kinaseUniRule annotation
    Short name:
    UMP/CMP kinaseUniRule annotation
    Short name:
    UMP/CMPKUniRule annotation
    Gene namesi
    Name:pyrKUniRule annotation
    Synonyms:ctpS
    ORF Names:DDB_G0287495
    OrganismiDictyostelium discoideum (Slime mold)
    Taxonomic identifieri44689 [NCBI]
    Taxonomic lineageiEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium
    ProteomesiUP000002195 Componentsi: Chromosome 5, Unassembled WGS sequence

    Organism-specific databases

    dictyBaseiDDB_G0287495. pyrK.

    Subcellular locationi

    • Cytoplasm UniRule annotation
    • Nucleus UniRule annotation

    GO - Cellular componenti

    • cytoplasm Source: UniProtKB-SubCell
    • intracellular Source: dictyBase
    • nucleus Source: UniProtKB-SubCell
    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 195195UMP-CMP kinasePRO_0000158948Add
    BLAST

    Proteomic databases

    PRIDEiP20425.

    Interactioni

    Subunit structurei

    Monomer.UniRule annotation2 Publications

    Protein-protein interaction databases

    STRINGi44689.DDB0191367.

    Structurei

    Secondary structure

    1
    195
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi8 – 158Combined sources
    Helixi20 – 3112Combined sources
    Beta strandi34 – 374Combined sources
    Helixi38 – 4710Combined sources
    Helixi53 – 619Combined sources
    Helixi68 – 8013Combined sources
    Beta strandi87 – 904Combined sources
    Helixi96 – 10611Combined sources
    Turni107 – 1093Combined sources
    Beta strandi111 – 1199Combined sources
    Helixi122 – 13312Combined sources
    Turni134 – 1363Combined sources
    Helixi143 – 15513Combined sources
    Helixi157 – 16610Combined sources
    Beta strandi170 – 1745Combined sources
    Helixi179 – 19214Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1QF9X-ray1.70A2-195[»]
    1UKEX-ray2.20A2-195[»]
    2UKDX-ray2.20A2-195[»]
    3UKDX-ray1.90A2-195[»]
    4UKDX-ray2.00A2-195[»]
    5UKDX-ray1.90A2-195[»]
    ProteinModelPortaliP20425.
    SMRiP20425. Positions 2-195.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP20425.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni37 – 6630NMPbindAdd
    BLAST
    Regioni131 – 14111LIDAdd
    BLAST

    Domaini

    Consists of three domains, a large central CORE domain and two small peripheral domains, NMPbind and LID, which undergo movements during catalysis. The LID domain closes over the site of phosphoryl transfer upon ATP binding. Assembling and dissambling the active center during each catalytic cycle provides an effective means to prevent ATP hydrolysis.

    Sequence similaritiesi

    Belongs to the adenylate kinase family. UMP-CMP kinase subfamily.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0563.
    InParanoidiP20425.
    KOiK13800.
    OMAiCTKPIID.
    PhylomeDBiP20425.

    Family and domain databases

    Gene3Di3.40.50.300. 1 hit.
    HAMAPiMF_00235. Adenylate_kinase_Adk.
    MF_03172. Adenylate_kinase_UMP_CMP_kin.
    InterProiIPR000850. Adenylat/UMP-CMP_kin.
    IPR027417. P-loop_NTPase.
    IPR006266. UMP_CMP_kinase.
    [Graphical view]
    PANTHERiPTHR23359. PTHR23359. 1 hit.
    PRINTSiPR00094. ADENYLTKNASE.
    SUPFAMiSSF52540. SSF52540. 1 hit.
    TIGRFAMsiTIGR01359. UMP_CMP_kin_fam. 1 hit.
    PROSITEiPS00113. ADENYLATE_KINASE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P20425-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MMEKSKPNVV FVLGGPGSGK GTQCANIVRD FGWVHLSAGD LLRQEQQSGS
    60 70 80 90 100
    KDGEMIATMI KNGEIVPSIV TVKLLKNAID ANQGKNFLVD GFPRNEENNN
    110 120 130 140 150
    SWEENMKDFV DTKFVLFFDC PEEVMTQRLL KRGESSGRSD DNIESIKKRF
    160 170 180 190
    NTFNVQTKLV IDHYNKFDKV KIIPANRDVN EVYNDVENLF KSMGF
    Length:195
    Mass (Da):22,074
    Last modified:December 4, 2007 - v2
    Checksum:i076C6780DDC1C0F0
    GO

    Sequence cautioni

    The sequence AAA33272.1 differs from that shown. Reason: Erroneous initiation. Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M34568 mRNA. Translation: AAA33272.1. Different initiation.
    AAFI02000102 Genomic DNA. Translation: EAL63690.1.
    PIRiA35235.
    RefSeqiXP_637196.1. XM_632104.1.

    Genome annotation databases

    EnsemblProtistsiDDB0191367; DDB0191367; DDB_G0287495.
    GeneIDi8626154.
    KEGGiddi:DDB_G0287495.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M34568 mRNA. Translation: AAA33272.1. Different initiation.
    AAFI02000102 Genomic DNA. Translation: EAL63690.1.
    PIRiA35235.
    RefSeqiXP_637196.1. XM_632104.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1QF9X-ray1.70A2-195[»]
    1UKEX-ray2.20A2-195[»]
    2UKDX-ray2.20A2-195[»]
    3UKDX-ray1.90A2-195[»]
    4UKDX-ray2.00A2-195[»]
    5UKDX-ray1.90A2-195[»]
    ProteinModelPortaliP20425.
    SMRiP20425. Positions 2-195.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi44689.DDB0191367.

    Proteomic databases

    PRIDEiP20425.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblProtistsiDDB0191367; DDB0191367; DDB_G0287495.
    GeneIDi8626154.
    KEGGiddi:DDB_G0287495.

    Organism-specific databases

    dictyBaseiDDB_G0287495. pyrK.

    Phylogenomic databases

    eggNOGiCOG0563.
    InParanoidiP20425.
    KOiK13800.
    OMAiCTKPIID.
    PhylomeDBiP20425.

    Enzyme and pathway databases

    BRENDAi2.7.4.14. 1939.
    ReactomeiREACT_339252. Synthesis and interconversion of nucleotide di- and triphosphates.
    SABIO-RKP20425.

    Miscellaneous databases

    EvolutionaryTraceiP20425.
    PROiP20425.

    Family and domain databases

    Gene3Di3.40.50.300. 1 hit.
    HAMAPiMF_00235. Adenylate_kinase_Adk.
    MF_03172. Adenylate_kinase_UMP_CMP_kin.
    InterProiIPR000850. Adenylat/UMP-CMP_kin.
    IPR027417. P-loop_NTPase.
    IPR006266. UMP_CMP_kinase.
    [Graphical view]
    PANTHERiPTHR23359. PTHR23359. 1 hit.
    PRINTSiPR00094. ADENYLTKNASE.
    SUPFAMiSSF52540. SSF52540. 1 hit.
    TIGRFAMsiTIGR01359. UMP_CMP_kin_fam. 1 hit.
    PROSITEiPS00113. ADENYLATE_KINASE. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "cDNA-derived sequence of UMP-CMP kinase from Dictyostelium discoideum and expression of the enzyme in Escherichia coli."
      Wiesmueller L., Noegel A.A., Barzu O., Gerisch G., Schleicher M.
      J. Biol. Chem. 265:6339-6345(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES.
    2. "The genome of the social amoeba Dictyostelium discoideum."
      Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R., Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B., Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T., Lehmann R., Hamlin N.
      , Davies R., Gaudet P., Fey P., Pilcher K., Chen G., Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N., Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E., Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N., Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D., Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T., Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D., Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A., Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M., Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A., Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y., Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C., Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R., Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.
      Nature 435:43-57(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: AX4.
    3. "Crystal structure of the complex of UMP/CMP kinase from Dictyostelium discoideum and the bisubstrate inhibitor P1-(5'-adenosyl) P5-(5'-uridyl) pentaphosphate (UP5A) and Mg2+ at 2.2-A: implications for water-mediated specificity."
      Scheffzek K., Kliche W., Wiesmuller L., Reinstein J.
      Biochemistry 35:9716-9727(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 2-195 IN COMPLEXES WITH SUBSTRATE ANALOGS, COFACTOR.
    4. "Structures of active conformations of UMP kinase from Dictyostelium discoideum suggest phosphoryl transfer is associative."
      Schlichting I., Reinstein J.
      Biochemistry 36:9290-9296(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 2-195IN COMPLEX WITH ADP; CMP AND UDP.
    5. "pH influences fluoride coordination number of the AlFx phosphoryl transfer transition state analog."
      Schlichting I., Reinstein J.
      Nat. Struct. Biol. 6:721-723(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 2-194 IN COMPLEX WITH ADP AND CMP.

    Entry informationi

    Entry nameiKCY_DICDI
    AccessioniPrimary (citable) accession number: P20425
    Secondary accession number(s): Q54KA2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1991
    Last sequence update: December 4, 2007
    Last modified: July 22, 2015
    This is version 117 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Dictyostelium discoideum
      Dictyostelium discoideum: entries, gene names and cross-references to dictyBase
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. 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.