Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

O04905 (KCY3_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 91. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
UMP-CMP kinase 3

EC=2.7.4.14
Alternative name(s):
Deoxycytidylate kinase
Short name=CK
Short name=dCMP kinase
Uridine monophosphate/cytidine monophosphate kinase
Short name=UMP/CMP kinase
Short name=UMP/CMPK
Gene names
Name:PYR6
Ordered Locus Names:At5g26667
ORF Names:T7I7.5
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length202 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. HAMAP-Rule MF_03172

Catalytic activity

ATP + (d)CMP = ADP + (d)CDP. Ref.1

ATP + UMP = ADP + UDP. Ref.1

Cofactor

Binds 1 magnesium ion per monomer By similarity. HAMAP-Rule MF_03172

Subunit structure

Monomer By similarity. HAMAP-Rule MF_03172

Subcellular location

Cytoplasm By similarity. Nucleus By similarity HAMAP-Rule MF_03172.

Domain

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 By similarity. HAMAP-Rule MF_03172

Sequence similarities

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

Biophysicochemical properties

Kinetic parameters:

KM=29.3 µM for ATP (with UMP as cosubstrate) Ref.1

KM=291.7 µM for ATP (with CMP as cosubstrate)

KM=152.9 µM for UMP

KM=266.4 µM for CMP

pH dependence:

Optimum pH is 6.5.

Mass spectrometry

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

Ontologies

Keywords
   Biological processPyrimidine biosynthesis
   Cellular componentCytoplasm
Nucleus
   Coding sequence diversityAlternative splicing
   LigandATP-binding
Nucleotide-binding
   Molecular functionKinase
Transferase
   Technical termComplete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processpyrimidine nucleotide biosynthetic process

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

nucleus

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionATP binding

Inferred from electronic annotation. Source: UniProtKB-KW

cytidylate kinase activity

Inferred from electronic annotation. Source: UniProtKB-EC

phosphotransferase activity, phosphate group as acceptor

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: O04905-1)

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.
Isoform 2 (identifier: O04905-2)

The sequence of this isoform differs from the canonical sequence as follows:
     201-202: EA → KLNSCAIL
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 202202UMP-CMP kinase 3 HAMAP-Rule MF_03172
PRO_0000158945

Regions

Nucleotide binding24 – 296ATP By similarity
Nucleotide binding71 – 733NMP By similarity
Nucleotide binding98 – 1014NMP By similarity
Region44 – 7330NMPbind By similarity
Region136 – 1449LID By similarity

Sites

Binding site501NMP By similarity
Binding site1051CMP By similarity
Binding site1371ATP By similarity
Binding site1411NMP By similarity
Binding site1521NMP By similarity
Binding site1801ATP; via carbonyl oxygen By similarity

Natural variations

Alternative sequence201 – 2022EA → KLNSCAIL in isoform 2.
VSP_053919

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified July 1, 1997. Version 1.
Checksum: 41AD0CFACD816315

FASTA20222,482
        10         20         30         40         50         60 
MGSVDAANGS GKKPTVIFVL GGPGSGKGTQ CAYIVEHYGY THLSAGDLLR AEIKSGSENG 

        70         80         90        100        110        120 
TMIQNMIKEG KIVPSEVTIK LLQKAIQENG NDKFLIDGFP RNEENRAAFE KVTEIEPKFV 

       130        140        150        160        170        180 
LFFDCPEEEM EKRLLGRNQG REDDNIETIR KRFKVFLESS LPVIHYYEAK GKVRKINAAK 

       190        200 
PIEAVFEEVK AIFSPEAEKV EA 

« Hide

Isoform 2 [UniParc].

Checksum: 5AF703F74D781B55
Show »

FASTA20823,125

References

« Hide 'large scale' references
[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. expand/collapse author list , 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 (ISOFORM 2).
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_001031942.1. NM_001036865.1. [O04905-1]
NP_850867.1. NM_180536.2. [O04905-2]
NP_850868.1. NM_180537.2. [O04905-1]
UniGeneAt.10397.

3D structure databases

ProteinModelPortalO04905.
SMRO04905. Positions 13-193.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid17985. 3 interactions.
IntActO04905. 3 interactions.
STRING3702.AT5G26667.1-P.

Proteomic databases

PaxDbO04905.
PRIDEO04905.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT5G26667.1; AT5G26667.1; AT5G26667. [O04905-2]
AT5G26667.2; AT5G26667.2; AT5G26667. [O04905-1]
AT5G26667.3; AT5G26667.3; AT5G26667. [O04905-1]
GeneID832710.
KEGGath:AT5G26667.

Organism-specific databases

TAIRAT5G26667.

Phylogenomic databases

eggNOGCOG0563.
HOGENOMHOG000238771.
InParanoidO04905.
KOK13800.
OMACAYIVEH.
PhylomeDBO04905.

Enzyme and pathway databases

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

Gene expression databases

GenevestigatorO04905.

Family and domain databases

Gene3D3.40.50.300. 1 hit.
HAMAPMF_00235. Adenylate_kinase_Adk.
MF_03172. Adenylate_kinase_UMP_CMP_kin.
InterProIPR000850. Adenylat/UMP-CMP_kin.
IPR027417. P-loop_NTPase.
IPR006266. UMP_CMP_kinase.
[Graphical view]
PANTHERPTHR23359. PTHR23359. 1 hit.
PRINTSPR00094. ADENYLTKNASE.
SUPFAMSSF52540. SSF52540. 1 hit.
TIGRFAMsTIGR01359. UMP_CMP_kin_fam. 1 hit.
PROSITEPS00113. ADENYLATE_KINASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameKCY3_ARATH
AccessionPrimary (citable) accession number: O04905
Secondary accession number(s): A0JQ75
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: July 1, 1997
Last modified: June 11, 2014
This is version 91 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names