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Protein

UMP-CMP kinase 3

Gene

UMK3

Organism
Arabidopsis thaliana (Mouse-ear cress)
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. 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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei50 – 501NMPUniRule annotation
    Binding sitei105 – 1051CMPUniRule annotation
    Binding sitei137 – 1371ATPUniRule annotation
    Binding sitei141 – 1411NMPUniRule annotation
    Binding sitei152 – 1521NMPUniRule annotation
    Binding sitei180 – 1801ATP; via carbonyl oxygenUniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi24 – 296ATPUniRule annotation
    Nucleotide bindingi71 – 733NMPUniRule annotation
    Nucleotide bindingi98 – 1014NMPUniRule annotation

    GO - Molecular functioni

    • ATP binding Source: UniProtKB
    • cytidylate kinase activity Source: UniProtKB
    • uridylate kinase activity Source: UniProtKB-HAMAP

    GO - Biological processi

    • 'de novo' pyrimidine nucleobase biosynthetic process Source: InterPro
    • nucleotide phosphorylation Source: GOC
    • pyrimidine nucleotide biosynthetic process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Kinase, Transferase

    Keywords - Biological processi

    Pyrimidine biosynthesis

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciARA:AT5G26667-MONOMER.
    ARA:GQT-645-MONOMER.
    ARA:GQT-724-MONOMER.
    MetaCyc:AT5G26667-MONOMER.
    BRENDAi2.7.4.14. 399.
    ReactomeiREACT_294404. Synthesis and 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
    ProteomesiUP000006548 Componenti: Chromosome 5

    Organism-specific databases

    TAIRiAT5G26667.

    Subcellular locationi

    • Cytoplasm UniRule annotation
    • Nucleus UniRule annotation

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 202202UMP-CMP kinase 3PRO_0000158945Add
    BLAST

    Proteomic databases

    PaxDbiO04905.
    PRIDEiO04905.

    Interactioni

    Subunit structurei

    Monomer.UniRule annotation

    Protein-protein interaction databases

    BioGridi17985. 3 interactions.
    IntActiO04905. 3 interactions.
    STRINGi3702.AT5G26667.1.

    Structurei

    3D structure databases

    ProteinModelPortaliO04905.
    SMRiO04905. Positions 13-193.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni44 – 7330NMPbindUniRule annotationAdd
    BLAST
    Regioni136 – 1449LIDUniRule annotation

    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

    eggNOGiCOG0563.
    HOGENOMiHOG000238771.
    InParanoidiO04905.
    KOiK13800.
    OMAiEHYNSKD.
    PhylomeDBiO04905.

    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]

    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)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei201 – 2022EA → KLNSCAIL in isoform 2. 1 PublicationVSP_053919

    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.
    BT029445 mRNA. Translation: ABK59674.1.
    RefSeqiNP_001031942.1. NM_001036865.1. [O04905-1]
    NP_850867.1. NM_180536.2. [O04905-2]
    NP_850868.1. NM_180537.2. [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]
    GeneIDi832710.
    KEGGiath:AT5G26667.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    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.
    BT029445 mRNA. Translation: ABK59674.1.
    RefSeqiNP_001031942.1. NM_001036865.1. [O04905-1]
    NP_850867.1. NM_180536.2. [O04905-2]
    NP_850868.1. NM_180537.2. [O04905-1]
    UniGeneiAt.10397.

    3D structure databases

    ProteinModelPortaliO04905.
    SMRiO04905. Positions 13-193.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi17985. 3 interactions.
    IntActiO04905. 3 interactions.
    STRINGi3702.AT5G26667.1.

    Proteomic databases

    PaxDbiO04905.
    PRIDEiO04905.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

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

    Organism-specific databases

    TAIRiAT5G26667.

    Phylogenomic databases

    eggNOGiCOG0563.
    HOGENOMiHOG000238771.
    InParanoidiO04905.
    KOiK13800.
    OMAiEHYNSKD.
    PhylomeDBiO04905.

    Enzyme and pathway databases

    BioCyciARA:AT5G26667-MONOMER.
    ARA:GQT-645-MONOMER.
    ARA:GQT-724-MONOMER.
    MetaCyc:AT5G26667-MONOMER.
    BRENDAi2.7.4.14. 399.
    ReactomeiREACT_294404. Synthesis and interconversion of nucleotide di- and triphosphates.

    Miscellaneous databases

    PROiO04905.

    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. "Cloning, expression in Escherichia coli, and characterization of Arabidopsis thaliana UMP/CMP kinase."
      Zhou L., Lacroute F., Thornburg R.
      Plant Physiol. 117:245-254(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), PROTEIN SEQUENCE OF 1-15, CATALYTIC ACTIVITY, MASS SPECTROMETRY, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, REACTION MECHANISM.
    2. "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana."
      Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E., Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.
      , Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L., O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D., Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M., Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L., Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B., Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P., Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M., Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D., Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A., Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I., Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T., Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A., McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U., Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M., Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G., Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W., Bevan M., Fransz P.F.
      Nature 408:823-826(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    3. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    4. "Arabidopsis ORF Clones."
      Bautista V.R., Kim C.J., Chen H., Quinitio C., Ecker J.R.
      Submitted (NOV-2006) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).

    Entry informationi

    Entry nameiKCY3_ARATH
    AccessioniPrimary (citable) accession number: O04905
    Secondary accession number(s): A0JQ75
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: July 1, 1997
    Last modified: July 22, 2015
    This is version 101 of the entry and version 1 of the sequence. [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

    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.