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P20425

- KCY_DICDI

UniProt

P20425 - KCY_DICDI

Protein

UMP-CMP kinase

Gene

pyrK

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 109 (01 Oct 2014)
      Sequence version 2 (04 Dec 2007)
      Previous versions | rss
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    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.1 PublicationUniRule annotation
    ATP + UMP = ADP + UDP.1 PublicationUniRule annotation

    Cofactori

    Binds 1 magnesium ion per monomer. The magnesium ion binds to water and substrates.1 PublicationUniRule annotation

    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 – 981CMP2 PublicationsUniRule annotation
    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

    1. ATP binding Source: dictyBase
    2. cytidylate kinase activity Source: dictyBase
    3. magnesium ion binding Source: dictyBase
    4. phosphotransferase activity, phosphate group as acceptor Source: dictyBase
    5. UMP kinase activity Source: dictyBase

    GO - Biological processi

    1. CDP biosynthetic process Source: dictyBase
    2. nucleotide salvage Source: dictyBase
    3. pyrimidine nucleobase salvage Source: dictyBase
    4. UDP biosynthetic process Source: dictyBase

    Keywords - Molecular functioni

    Kinase, Transferase

    Keywords - Biological processi

    Pyrimidine biosynthesis

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    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: Chromosome 5, UP000002195: Unassembled WGS sequence

    Organism-specific databases

    dictyBaseiDDB_G0287495. pyrK.

    Subcellular locationi

    Cytoplasm UniRule annotation. Nucleus UniRule annotation

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell
    2. intracellular Source: dictyBase
    3. nucleus Source: UniProtKB-SubCell

    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.2 PublicationsUniRule annotation

    Protein-protein interaction databases

    STRINGi44689.DDB_0191367.

    Structurei

    Secondary structure

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

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    KOiK13800.
    OMAiKRPGSQY.
    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

    MMEKSKPNVV FVLGGPGSGK GTQCANIVRD FGWVHLSAGD LLRQEQQSGS    50
    KDGEMIATMI KNGEIVPSIV TVKLLKNAID ANQGKNFLVD GFPRNEENNN 100
    SWEENMKDFV DTKFVLFFDC PEEVMTQRLL KRGESSGRSD DNIESIKKRF 150
    NTFNVQTKLV IDHYNKFDKV KIIPANRDVN EVYNDVENLF KSMGF 195
    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.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M34568 mRNA. Translation: AAA33272.1 . Different initiation.
    AAFI02000102 Genomic DNA. Translation: EAL63690.1 .
    PIRi A35235.
    RefSeqi XP_637196.1. XM_632104.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1QF9 X-ray 1.70 A 2-195 [» ]
    1UKE X-ray 2.20 A 2-195 [» ]
    2UKD X-ray 2.20 A 2-195 [» ]
    3UKD X-ray 1.90 A 2-195 [» ]
    4UKD X-ray 2.00 A 2-195 [» ]
    5UKD X-ray 1.90 A 2-195 [» ]
    ProteinModelPortali P20425.
    SMRi P20425. Positions 2-195.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 44689.DDB_0191367.

    Proteomic databases

    PRIDEi P20425.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblProtistsi DDB0191367 ; DDB0191367 ; DDB_G0287495 .
    GeneIDi 8626154.
    KEGGi ddi:DDB_G0287495.

    Organism-specific databases

    dictyBasei DDB_G0287495. pyrK.

    Phylogenomic databases

    eggNOGi COG0563.
    KOi K13800.
    OMAi KRPGSQY.
    PhylomeDBi P20425.

    Enzyme and pathway databases

    SABIO-RK P20425.

    Miscellaneous databases

    EvolutionaryTracei P20425.
    PROi P20425.

    Family and domain databases

    Gene3Di 3.40.50.300. 1 hit.
    HAMAPi MF_00235. Adenylate_kinase_Adk.
    MF_03172. Adenylate_kinase_UMP_CMP_kin.
    InterProi IPR000850. Adenylat/UMP-CMP_kin.
    IPR027417. P-loop_NTPase.
    IPR006266. UMP_CMP_kinase.
    [Graphical view ]
    PANTHERi PTHR23359. PTHR23359. 1 hit.
    PRINTSi PR00094. ADENYLTKNASE.
    SUPFAMi SSF52540. SSF52540. 1 hit.
    TIGRFAMsi TIGR01359. UMP_CMP_kin_fam. 1 hit.
    PROSITEi PS00113. ADENYLATE_KINASE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 109 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