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O04905

- KCY3_ARATH

UniProt

O04905 - KCY3_ARATH

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Protein

UMP-CMP kinase 3

Gene

UMK3

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - 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.1 PublicationUniRule annotation
ATP + UMP = ADP + UDP.1 PublicationUniRule annotation

Cofactori

Binds 1 magnesium 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

  1. ATP binding Source: UniProtKB
  2. cytidylate kinase activity Source: UniProtKB
  3. uridylate kinase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. 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.

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: Chromosome 5

Organism-specific databases

TAIRiAT5G26667.

Subcellular locationi

Cytoplasm UniRule annotation. Nucleus UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-HAMAP
  2. nucleus Source: UniProtKB-HAMAP
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.

Expressioni

Gene expression databases

GenevestigatoriO04905.

Interactioni

Subunit structurei

Monomer.UniRule annotation

Protein-protein interaction databases

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

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.
OMAiCAYIVEH.
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. Align

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:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
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 .
RefSeqi NP_001031942.1. NM_001036865.1. [O04905-1 ]
NP_850867.1. NM_180536.2. [O04905-2 ]
NP_850868.1. NM_180537.2. [O04905-1 ]
UniGenei At.10397.

3D structure databases

ProteinModelPortali O04905.
SMRi O04905. Positions 13-193.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 17985. 3 interactions.
IntActi O04905. 3 interactions.
STRINGi 3702.AT5G26667.1-P.

Proteomic databases

PaxDbi O04905.
PRIDEi O04905.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblPlantsi AT5G26667.1 ; AT5G26667.1 ; AT5G26667 . [O04905-2 ]
AT5G26667.2 ; AT5G26667.2 ; AT5G26667 . [O04905-1 ]
AT5G26667.3 ; AT5G26667.3 ; AT5G26667 . [O04905-1 ]
GeneIDi 832710.
KEGGi ath:AT5G26667.

Organism-specific databases

TAIRi AT5G26667.

Phylogenomic databases

eggNOGi COG0563.
HOGENOMi HOG000238771.
InParanoidi O04905.
KOi K13800.
OMAi CAYIVEH.
PhylomeDBi O04905.

Enzyme and pathway databases

BioCyci ARA:AT5G26667-MONOMER.
ARA:GQT-645-MONOMER.
ARA:GQT-724-MONOMER.
MetaCyc:AT5G26667-MONOMER.

Gene expression databases

Genevestigatori O04905.

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

« 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: October 29, 2014
This is version 94 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