Q8U122 (PYRH_PYRFU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Uridylate kinase
Short name=UK
EC=2.7.4.22

Alternative name(s):
Uridine monophosphate kinase
Short name=UMP kinase
Short name=UMPK

Gene names

Name:	pyrH
Ordered Locus Names:	PF1407

Organism

Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Taxonomic identifier

186497 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Pyrococcus

Protein attributes

Sequence length	225 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the reversible phosphorylation of UMP to UDP, with ATP as the most efficient phosphate donor. Ref.2
Catalytic activity	ATP + UMP = ADP + UDP. HAMAP MF_01220_A
Enzyme regulation	Inhibited by UTP By similarity. HAMAP MF_01220_A
Pathway	Pyrimidine metabolism; CTP biosynthesis via de novo pathway; UDP from UMP (UMPK route): step 1/1. HAMAP MF_01220_A
Subunit structure	Homohexamer; trimer of dimers. Ref.3
Subcellular location	Cytoplasm By similarity HAMAP MF_01220_A.
Sequence similarities	Belongs to the UMP kinase family.

Ontologies

Keywords
Biological process	Pyrimidine biosynthesis
Cellular component	Cytoplasm
Ligand	ATP-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Kinase Transferase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	cellular amino acid biosynthetic process Inferred from electronic annotation. Source: InterPro pyrimidine nucleotide biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW UMP kinase activity Inferred from electronic annotation. Source: EC metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 225

225

Uridylate kinase HAMAP MF_01220_A

PRO_0000143923

Regions

Nucleotide binding

9 – 10

2

ATP HAMAP MF_01220_A

Nucleotide binding

114 – 120

7

UMP HAMAP MF_01220_A

Sites

Metal binding

6

1

Magnesium 1

Metal binding

120

1

Magnesium 1

Metal binding

121

1

Magnesium 1

Metal binding

121

1

Magnesium 2

Metal binding

182

1

Magnesium 2; via carbonyl oxygen

Binding site

44

1

UMP; via amide nitrogen

Binding site

45

1

ATP; via amide nitrogen

Binding site

49

1

ATP By similarity

Binding site

66

1

UMP

Binding site

140

1

ATP

Binding site

141

1

ATP

Binding site

146

1

ATP; via amide nitrogen and carbonyl oxygen

Binding site

149

1

ATP

Binding site

179

1

UMP; via amide nitrogen

Binding site

182

1

ATP; via amide nitrogen

Secondary structure

1

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225

Helix Strand Turn

Details...

Beta strand

2 – 7

6

Helix

9 – 12

4

Beta strand

14 – 16

3

Helix

19 – 35

17

Beta strand

36 – 42

7

Helix

45 – 56

12

Turn

57 – 59

3

Helix

62 – 84

23

Helix

85 – 87

3

Helix

96 – 104

9

Helix

120 – 130

11

Beta strand

134 – 139

6

Beta strand

141 – 144

4

Beta strand

146 – 148

3

Turn

150 – 152

3

Beta strand

160 – 162

3

Helix

164 – 172

9

Helix

186 – 195

10

Beta strand

199 – 202

4

Helix

204 – 207

4

Helix

210 – 214

5

Beta strand

218 – 223

6

Sequences

	Sequence		Length	Mass (Da)
	Q8U122 [UniParc]. Last modified June 1, 2002. Version 1. Checksum: 510D151A02F8D534	FASTA	225	24,491
	10 20 30 40 50 60 MRIVFDIGGS VLVPENPDID FIKEIAYQLT KVSEDHEVAV VVGGGKLARK YIEVAEKFNS 70 80 90 100 110 120 SETFKDFIGI QITRANAMLL IAALREKAYP VVVEDFWEAW KAVQLKKIPV MGGTHPGHTT 130 140 150 160 170 180 DAVAALLAEF LKADLLVVIT NVDGVYTADP KKDPTAKKIK KMKPEELLEI VGKGIEKAGS 190 200 210 220 SSVIDPLAAK IIARSGIKTI VIGKEDAKDL FRVIKGDHNG TTIEP

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences." Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M., DiRuggiero J., Robb F.T. Genetics 152:1299-1305(1999) [PubMed: 10430560] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
[2]	"First-time crystallization and preliminary X-ray crystallographic analysis of a bacterial-archaeal type UMP kinase, a key enzyme in microbial pyrimidine biosynthesis." Marco-Marin C., Escamilla-Honrubia J.M., Rubio V. Biochim. Biophys. Acta 1747:271-275(2005) [PubMed: 15698963] [Abstract] Cited for: FUNCTION, SUBSTRATE SPECIFICITY, CRYSTALLIZATION. Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
[3]	"The crystal structure of Pyrococcus furiosus UMP kinase provides insight into catalysis and regulation in microbial pyrimidine nucleotide biosynthesis." Marco-Marin C., Gil-Ortiz F., Rubio V. J. Mol. Biol. 352:438-454(2005) [PubMed: 16095620] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH UMP; ATP ANALOG AND MAGNESIUM, SUBUNIT. Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
[4]	"Structure of UMP kinase from Pyrococcus furiosus complexed with UTP." Marco-Marin C., Rubio V. Submitted (OCT-2007) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (2.45 ANGSTROMS) IN COMPLEX WITH UTP. Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE009950 Genomic DNA. Translation: AAL81531.1.

RefSeq

NP_579136.1. NC_003413.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2BMU	X-ray	2.55	A/B	1-225	[»]
2BRI	X-ray	3.00	A/B	1-225	[»]
2BRX	X-ray	2.40	A/B	1-225	[»]
2JI5	X-ray	2.45	A/B	1-225	[»]

ProteinModelPortal

Q8U122.

SMR

Q8U122. Positions 1-225.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBPYRT00000005887; EBPYRP00000005748; EBPYRG00000005886.

GeneID

1469283.

GenomeReviews

Gene locus PF1407 in contig AE009950_GR.

KEGG

pfu:PF1407.

NMPDR

fig|186497.1.peg.1454.

Phylogenomic databases

GeneTree

EBGT00050000022456.

HOGENOM

HBG497552.

OMA

TRANAML.

ProtClustDB

PRK00358.

Enzyme and pathway databases

BRENDA

2.7.4.22. 5243.

Family and domain databases

HAMAP

MF_01220_A. PyrH_A.
[Tree]

InterPro

IPR001048. Asp/Glu/Uridylate_kinase.
IPR011817. Uridylate_kinase.
IPR011818. Uridylate_kinase_arch/spir.
[Graphical view]

Gene3D

G3DSA:3.40.1160.10. Aa_kinase. 1 hit.

KO

K09903.

Pfam

PF00696. AA_kinase. 1 hit.
[Graphical view]

PIRSF

PIRSF005650. Uridylate_kin. 1 hit.

SUPFAM

SSF53633. Aa_kinase. 1 hit.

TIGRFAMs

TIGR02076. PyrH_arch. 1 hit.

ProtoNet

Search...

Entry information

Entry name

PYRH_PYRFU

Accession

Primary (citable) accession number: Q8U122

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 30, 2002
Last sequence update:	June 1, 2002
Last modified:	November 16, 2011
This is version 57 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program