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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.UniRule annotation1 Publication

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 Mg2+ 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)DescriptionActionsGraphical viewLength
    Binding sitei43NMPUniRule annotation3 Publications1
    Binding sitei98CMPUniRule annotation2 Publications1
    Binding sitei132ATPUniRule annotation3 Publications1
    Binding sitei138NMPUniRule annotation2 Publications1
    Binding sitei149NMPUniRule annotation3 Publications1
    Binding sitei177ATP; via carbonyl oxygenUniRule annotation3 Publications1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi17 – 22ATPUniRule annotation3 Publications6
    Nucleotide bindingi64 – 66NMPUniRule annotation3 Publications3
    Nucleotide bindingi91 – 94NMPUniRule annotation3 Publications4

    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 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.
    ReactomeiR-DDI-499943. 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
    Proteomesi
    • UP000002195 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)DescriptionActionsGraphical viewLength
    ChainiPRO_00001589481 – 195UMP-CMP kinaseAdd BLAST195

    Proteomic databases

    PaxDbiP20425.
    PRIDEiP20425.

    Interactioni

    Subunit structurei

    Monomer.UniRule annotation2 Publications

    Protein-protein interaction databases

    STRINGi44689.DDB0191367.

    Structurei

    Secondary structure

    1195
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi8 – 15Combined sources8
    Helixi20 – 31Combined sources12
    Beta strandi34 – 37Combined sources4
    Helixi38 – 47Combined sources10
    Helixi53 – 61Combined sources9
    Helixi68 – 80Combined sources13
    Beta strandi87 – 90Combined sources4
    Helixi96 – 106Combined sources11
    Turni107 – 109Combined sources3
    Beta strandi111 – 119Combined sources9
    Helixi122 – 133Combined sources12
    Turni134 – 136Combined sources3
    Helixi143 – 155Combined sources13
    Helixi157 – 166Combined sources10
    Beta strandi170 – 174Combined sources5
    Helixi179 – 192Combined sources14

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiP20425.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni37 – 66NMPbindUniRule annotation3 PublicationsAdd BLAST30
    Regioni131 – 141LIDUniRule annotation3 PublicationsAdd BLAST11

    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.UniRule annotation3 Publications

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiKOG3079. Eukaryota.
    COG0563. LUCA.
    InParanoidiP20425.
    KOiK13800.
    OMAiMIATMIK.
    PhylomeDBiP20425.

    Family and domain databases

    CDDicd01428. ADK. 1 hit.
    Gene3Di3.40.50.300. 1 hit.
    HAMAPiMF_00235. Adenylate_kinase_Adk. 1 hit.
    MF_03172. Adenylate_kinase_UMP_CMP_kin. 1 hit.
    InterProiIPR000850. Adenylat/UMP-CMP_kin.
    IPR033690. Adenylat_kinase_CS.
    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 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

    EnsemblProtistsiEAL63690; EAL63690; 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
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi44689.DDB0191367.

    Proteomic databases

    PaxDbiP20425.
    PRIDEiP20425.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblProtistsiEAL63690; EAL63690; DDB_G0287495.
    GeneIDi8626154.
    KEGGiddi:DDB_G0287495.

    Organism-specific databases

    dictyBaseiDDB_G0287495. pyrK.

    Phylogenomic databases

    eggNOGiKOG3079. Eukaryota.
    COG0563. LUCA.
    InParanoidiP20425.
    KOiK13800.
    OMAiMIATMIK.
    PhylomeDBiP20425.

    Enzyme and pathway databases

    BRENDAi2.7.4.14. 1939.
    ReactomeiR-DDI-499943. Synthesis and interconversion of nucleotide di- and triphosphates.
    SABIO-RKP20425.

    Miscellaneous databases

    EvolutionaryTraceiP20425.
    PROiP20425.

    Family and domain databases

    CDDicd01428. ADK. 1 hit.
    Gene3Di3.40.50.300. 1 hit.
    HAMAPiMF_00235. Adenylate_kinase_Adk. 1 hit.
    MF_03172. Adenylate_kinase_UMP_CMP_kin. 1 hit.
    InterProiIPR000850. Adenylat/UMP-CMP_kin.
    IPR033690. Adenylat_kinase_CS.
    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...

    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: November 30, 2016
    This is version 127 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

    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.