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Protein

UMP-CMP kinase 3

Gene

UMK3

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: -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. Does not act on dCMP and dUMP.

Catalytic activityi

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

Cofactori

Mg2+UniRule annotationNote: Binds 1 Mg2+ ion per monomer.UniRule annotation

Kineticsi

  1. KM=29.3 µM for ATP (with UMP as cosubstrate)1 Publication
  2. KM=291.7 µM for ATP (with CMP as cosubstrate)1 Publication
  3. KM=152.9 µM for UMP1 Publication
  4. KM=266.4 µM for CMP1 Publication

    pH dependencei

    Optimum pH is 6.5.1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei50NMPUniRule annotation1
    Binding sitei105CMPUniRule annotation1
    Binding sitei137ATPUniRule annotation1
    Binding sitei141NMPUniRule annotation1
    Binding sitei152NMPUniRule annotation1
    Binding sitei180ATP; via carbonyl oxygenUniRule annotation1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi24 – 29ATPUniRule annotation6
    Nucleotide bindingi71 – 73NMPUniRule annotation3
    Nucleotide bindingi98 – 101NMPUniRule annotation4

    GO - Molecular functioni

    • ATP binding Source: UniProtKB
    • cytidylate kinase activity Source: UniProtKB
    • uridylate kinase activity Source: TAIR

    GO - Biological processi

    • 'de novo' pyrimidine nucleobase biosynthetic process Source: InterPro
    • pyrimidine nucleotide biosynthetic process Source: UniProtKB
    • pyrimidine ribonucleoside monophosphate metabolic process Source: TAIR

    Keywordsi

    Molecular functionKinase, Transferase
    Biological processPyrimidine biosynthesis
    LigandATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciARA:AT5G26667-MONOMER
    MetaCyc:AT5G26667-MONOMER
    BRENDAi2.7.4.14 399
    ReactomeiR-ATH-499943 Interconversion of nucleotide di- and triphosphates

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    UMP-CMP kinase 3UniRule 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:UMK3
    Synonyms:PYR6
    Ordered Locus Names:At5g26667
    ORF Names:T7I7.5
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    Proteomesi
    • UP000006548 Componenti: Chromosome 5

    Organism-specific databases

    AraportiAT5G26667
    TAIRilocus:1005716878 AT5G26667

    Subcellular locationi

    Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte; Source: COMPARTMENTS

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001589451 – 202UMP-CMP kinase 3Add BLAST202

    Proteomic databases

    PaxDbiO04905
    PRIDEiO04905

    PTM databases

    iPTMnetiO04905

    Expressioni

    Gene expression databases

    ExpressionAtlasiO04905 baseline and differential

    Interactioni

    Subunit structurei

    Monomer.UniRule annotation

    Protein-protein interaction databases

    BioGridi17985, 3 interactors
    IntActiO04905, 3 interactors
    STRINGi3702.AT5G26667.1

    Structurei

    3D structure databases

    ProteinModelPortaliO04905
    SMRiO04905
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni44 – 73NMPbindUniRule annotationAdd BLAST30
    Regioni136 – 144LIDUniRule annotation9

    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 annotation

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiKOG3079 Eukaryota
    COG0563 LUCA
    HOGENOMiHOG000238771
    InParanoidiO04905
    KOiK13800
    OMAiFCHLSAG
    OrthoDBiEOG09360KWD
    PhylomeDBiO04905

    Family and domain databases

    CDDicd01428 ADK, 1 hit
    HAMAPiMF_00235 Adenylate_kinase_Adk, 1 hit
    MF_03172 Adenylate_kinase_UMP_CMP_kin, 1 hit
    InterProiView protein in InterPro
    IPR000850 Adenylat/UMP-CMP_kin
    IPR033690 Adenylat_kinase_CS
    IPR027417 P-loop_NTPase
    IPR006266 UMP_CMP_kinase
    PANTHERiPTHR23359 PTHR23359, 1 hit
    PRINTSiPR00094 ADENYLTKNASE
    SUPFAMiSSF52540 SSF52540, 1 hit
    TIGRFAMsiTIGR01359 UMP_CMP_kin_fam, 1 hit
    PROSITEiView protein in PROSITE
    PS00113 ADENYLATE_KINASE, 1 hit

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

    Isoform 1 (identifier: O04905-1) [UniParc]FASTAAdd to basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

            10         20         30         40         50
    MGSVDAANGS GKKPTVIFVL GGPGSGKGTQ CAYIVEHYGY THLSAGDLLR
    60 70 80 90 100
    AEIKSGSENG TMIQNMIKEG KIVPSEVTIK LLQKAIQENG NDKFLIDGFP
    110 120 130 140 150
    RNEENRAAFE KVTEIEPKFV LFFDCPEEEM EKRLLGRNQG REDDNIETIR
    160 170 180 190 200
    KRFKVFLESS LPVIHYYEAK GKVRKINAAK PIEAVFEEVK AIFSPEAEKV

    EA
    Length:202
    Mass (Da):22,482
    Last modified:July 1, 1997 - v1
    Checksum:i41AD0CFACD816315
    GO
    Isoform 2 (identifier: O04905-2) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         201-202: EA → KLNSCAIL

    Note: No experimental confirmation available.
    Show »
    Length:208
    Mass (Da):23,125
    Checksum:i5AF703F74D781B55
    GO

    Mass spectrometryi

    Molecular mass is 22405±185 Da from positions 1 - 202. Determined by MALDI. 1 Publication

    Alternative sequence

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Alternative sequenceiVSP_053919201 – 202EA → KLNSCAIL in isoform 2. 1 Publication2

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF000147 mRNA Translation: AAB71135.1
    AC137518 Genomic DNA No translation available.
    CP002688 Genomic DNA Translation: AED93558.1
    CP002688 Genomic DNA Translation: AED93559.1
    CP002688 Genomic DNA Translation: AED93560.1
    CP002688 Genomic DNA Translation: ANM70813.1
    BT029445 mRNA Translation: ABK59674.1
    RefSeqiNP_001031942.1, NM_001036865.1 [O04905-1]
    NP_001332394.1, NM_001343973.1 [O04905-1]
    NP_850867.1, NM_180536.3 [O04905-2]
    NP_850868.1, NM_180537.3 [O04905-1]
    UniGeneiAt.10397

    Genome annotation databases

    EnsemblPlantsiAT5G26667.1; AT5G26667.1; AT5G26667 [O04905-2]
    AT5G26667.2; AT5G26667.2; AT5G26667 [O04905-1]
    AT5G26667.3; AT5G26667.3; AT5G26667 [O04905-1]
    AT5G26667.4; AT5G26667.4; AT5G26667 [O04905-1]
    GeneIDi832710
    GrameneiAT5G26667.1; AT5G26667.1; AT5G26667 [O04905-2]
    AT5G26667.2; AT5G26667.2; AT5G26667 [O04905-1]
    AT5G26667.3; AT5G26667.3; AT5G26667 [O04905-1]
    AT5G26667.4; AT5G26667.4; AT5G26667 [O04905-1]
    KEGGiath:AT5G26667

    Keywords - Coding sequence diversityi

    Alternative splicing

    Similar proteinsi

    Entry informationi

    Entry nameiKCY3_ARATH
    AccessioniPrimary (citable) accession number: O04905
    Secondary accession number(s): A0JQ75
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: July 1, 1997
    Last modified: April 25, 2018
    This is version 121 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. SIMILARITY comments
      Index of protein domains and families

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