UMP-CMP kinase - Dictyostelium discoideum (Slime mold)

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P20425 (KCY_DICDI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 29, 2013. Version 101. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
UMP-CMP kinase
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:	pyrK
Synonyms:	ctpS
ORF Names:	DDB_G0287495

Organism

Dictyostelium discoideum (Slime mold) [Reference proteome]

Taxonomic identifier

44689 [NCBI]

Taxonomic lineage

Eukaryota › Amoebozoa › Mycetozoa › Dictyosteliida › Dictyostelium

Protein attributes

Sequence length	195 AA.
Sequence status	Complete.
Protein existence	Evidence 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. 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. The magnesium ion binds to water and substrates. Ref.3
Subunit structure	Monomer.
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. HAMAP-Rule MF_03172
Sequence similarities	Belongs to the adenylate kinase family. UMP-CMP kinase subfamily.
Biophysicochemical properties	Kinetic parameters: K_M=25 µM for ATP Ref.1 K_M=0.4 mM for UMP K_M=0.1 mM for CMP
Sequence caution	The sequence AAA33272.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Biological process	Pyrimidine biosynthesis
Cellular component	Cytoplasm Nucleus
Ligand	ATP-binding Nucleotide-binding
Molecular function	Kinase Transferase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	CDP biosynthetic process Inferred from direct assay Ref.1. Source: dictyBase UDP biosynthetic process Inferred from direct assay Ref.1. Source: dictyBase nucleotide salvage Inferred from direct assay Ref.1. Source: dictyBase pyrimidine nucleobase salvage Inferred from direct assay Ref.3. Source: dictyBase
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell intracellular Inferred by curator Ref.1. Source: dictyBase nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from direct assay Ref.1 Ref.3. Source: dictyBase UMP kinase activity Inferred from direct assay Ref.1. Source: dictyBase cytidylate kinase activity Inferred from direct assay Ref.1. Source: dictyBase magnesium ion binding Inferred from direct assay Ref.3. Source: dictyBase
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 195

195

UMP-CMP kinase HAMAP-Rule MF_03172

PRO_0000158948

Regions

Nucleotide binding

17 – 22

ATP HAMAP-Rule MF_03172

Nucleotide binding

64 – 66

NMP HAMAP-Rule MF_03172

Nucleotide binding

91 – 94

NMP HAMAP-Rule MF_03172

Region

37 – 66

NMPbind HAMAP-Rule MF_03172

Region

131 – 141

LID HAMAP-Rule MF_03172

Sites

Binding site

NMP

Binding site

CMP

Binding site

132

ATP

Binding site

138

NMP

Binding site

149

NMP

Binding site

177

ATP; via carbonyl oxygen

Secondary structure

195

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P20425 [UniParc].

Last modified December 4, 2007. Version 2.
Checksum: 076C6780DDC1C0F0
Show »

FASTA

195

22,074

        10         20         30         40         50         60 
MMEKSKPNVV FVLGGPGSGK GTQCANIVRD FGWVHLSAGD LLRQEQQSGS KDGEMIATMI 

        70         80         90        100        110        120 
KNGEIVPSIV TVKLLKNAID ANQGKNFLVD GFPRNEENNN SWEENMKDFV DTKFVLFFDC 

       130        140        150        160        170        180 
PEEVMTQRLL KRGESSGRSD DNIESIKKRF NTFNVQTKLV IDHYNKFDKV KIIPANRDVN 

       190 
EVYNDVENLF KSMGF

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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. 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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M34568 mRNA. Translation: AAA33272.1. Different initiation.
AAFI02000102 Genomic DNA. Translation: EAL63690.1.

PIR

A35235.

RefSeq

XP_637196.1. XM_632104.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1QF9	X-ray	1.70	A	2-194	[»]
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	2-194	[»]

ProteinModelPortal

P20425.

SMR

P20425. Positions 2-195.

ModBase

Search...

Protein-protein interaction databases

STRING

44689.DDB_0191367.

Proteomic databases

PRIDE

P20425.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblProtists

DDB0191367; DDB0191367; DDB_G0287495.

GeneID

8626154.

KEGG

ddi:DDB_G0287495.

Organism-specific databases

dictyBase

DDB_G0287495. pyrK.

Phylogenomic databases

eggNOG

COG0563.

K13800.

OMA

FFDCDNE.

Enzyme and pathway databases

SABIO-RK

P20425.

Family and domain databases

HAMAP

MF_00235. Adenylate_kinase_Adk.
MF_03172. Adenylate_kinase_UMP_CMP_kin.

InterPro

IPR000850. Adenylate_kin.
IPR027417. P-loop_NTPase.
IPR006266. UMP_CMP_kinase.
[Graphical view]

PANTHER

PTHR23359. PTHR23359. 1 hit.

Pfam

PF00406. ADK. 1 hit.
[Graphical view]

PRINTS

PR00094. ADENYLTKNASE.

SUPFAM

SSF52540. SSF52540. 1 hit.

TIGRFAMs

TIGR01359. UMP_CMP_kin_fam. 1 hit.

PROSITE

PS00113. ADENYLATE_KINASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P20425.

Entry information

Entry name

KCY_DICDI

Accession

Primary (citable) accession number: P20425
Secondary accession number(s): Q54KA2

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1991
Last sequence update:	December 4, 2007
Last modified:	May 29, 2013
This is version 101 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Relevant documents

Dictyostelium discoideum

Dictyostelium discoideum: entries, gene names and cross-references to dictyBase

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Other

Entry information

Relevant documents