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Protein

Uridylate kinase

Gene

pyrH

Organism
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the reversible phosphorylation of UMP to UDP, with ATP as the most efficient phosphate donor.1 Publication

Catalytic activityi

ATP + UMP = ADP + UDP.

Enzyme regulationi

Inhibited by UTP.By similarity

Pathwayi: CTP biosynthesis via de novo pathway

This protein is involved in step 1 of the subpathway that synthesizes UDP from UMP (UMPK route).
Proteins known to be involved in this subpathway in this organism are:
  1. Uridylate kinase (pyrH)
This subpathway is part of the pathway CTP biosynthesis via de novo pathway, which is itself part of Pyrimidine metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes UDP from UMP (UMPK route), the pathway CTP biosynthesis via de novo pathway and in Pyrimidine metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi6 – 61Magnesium 11 Publication
Binding sitei44 – 441UMP; via amide nitrogen1 Publication
Binding sitei45 – 451ATP; via amide nitrogen
Binding sitei49 – 491ATPBy similarity
Binding sitei66 – 661UMP1 Publication
Metal bindingi120 – 1201Magnesium 11 Publication
Metal bindingi121 – 1211Magnesium 11 Publication
Metal bindingi121 – 1211Magnesium 21 Publication
Binding sitei140 – 1401ATP
Binding sitei141 – 1411ATP
Binding sitei146 – 1461ATP; via amide nitrogen and carbonyl oxygen
Binding sitei149 – 1491ATP
Binding sitei179 – 1791UMP; via amide nitrogen1 Publication
Metal bindingi182 – 1821Magnesium 2; via carbonyl oxygen1 Publication
Binding sitei182 – 1821ATP; via amide nitrogen

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi9 – 102ATP
Nucleotide bindingi114 – 1207UMP1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Biological processi

Pyrimidine biosynthesis

Keywords - Ligandi

ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BRENDAi2.7.4.22. 5243.
UniPathwayiUPA00159; UER00275.

Names & Taxonomyi

Protein namesi
Recommended name:
Uridylate kinase (EC:2.7.4.22)
Short name:
UK
Alternative name(s):
Uridine monophosphate kinase
Short name:
UMP kinase
Short name:
UMPK
Gene namesi
Name:pyrH
Ordered Locus Names:PF1407
OrganismiPyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Taxonomic identifieri186497 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
Proteomesi
  • UP000001013 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 225225Uridylate kinasePRO_0000143923Add
BLAST

Proteomic databases

PRIDEiQ8U122.

Interactioni

Subunit structurei

Homohexamer; trimer of dimers.2 Publications

Protein-protein interaction databases

STRINGi186497.PF1407.

Structurei

Secondary structure

1
225
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 76Combined sources
Helixi9 – 124Combined sources
Beta strandi14 – 163Combined sources
Helixi19 – 3517Combined sources
Beta strandi36 – 427Combined sources
Helixi45 – 5612Combined sources
Turni57 – 593Combined sources
Helixi62 – 8423Combined sources
Helixi85 – 873Combined sources
Helixi96 – 1049Combined sources
Beta strandi115 – 1184Combined sources
Helixi120 – 13011Combined sources
Beta strandi134 – 1396Combined sources
Beta strandi141 – 1444Combined sources
Beta strandi146 – 1483Combined sources
Turni150 – 1523Combined sources
Beta strandi160 – 1623Combined sources
Helixi164 – 1729Combined sources
Beta strandi182 – 1843Combined sources
Helixi186 – 19510Combined sources
Beta strandi199 – 2024Combined sources
Helixi204 – 2074Combined sources
Helixi210 – 2145Combined sources
Beta strandi218 – 2236Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2BMUX-ray2.55A/B1-225[»]
2BRIX-ray3.00A/B1-225[»]
2BRXX-ray2.40A/B1-225[»]
2JI5X-ray2.45A/B1-225[»]
ProteinModelPortaliQ8U122.
SMRiQ8U122. Positions 1-225.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8U122.

Family & Domainsi

Sequence similaritiesi

Belongs to the UMP kinase family.Curated

Phylogenomic databases

eggNOGiarCOG00858. Archaea.
COG0528. LUCA.
HOGENOMiHOG000047188.
KOiK09903.
OMAiGIHITRA.

Family and domain databases

Gene3Di3.40.1160.10. 1 hit.
HAMAPiMF_01220_A. PyrH_A.
InterProiIPR001048. Asp/Glu/Uridylate_kinase.
IPR011817. Uridylate_kinase.
IPR011818. Uridylate_kinase_arch/spir.
[Graphical view]
PANTHERiPTHR21499:SF23. PTHR21499:SF23. 1 hit.
PfamiPF00696. AA_kinase. 1 hit.
[Graphical view]
PIRSFiPIRSF005650. Uridylate_kin. 1 hit.
SUPFAMiSSF53633. SSF53633. 1 hit.
TIGRFAMsiTIGR02076. pyrH_arch. 1 hit.

Sequencei

Sequence statusi: Complete.

Q8U122-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRIVFDIGGS VLVPENPDID FIKEIAYQLT KVSEDHEVAV VVGGGKLARK
60 70 80 90 100
YIEVAEKFNS SETFKDFIGI QITRANAMLL IAALREKAYP VVVEDFWEAW
110 120 130 140 150
KAVQLKKIPV MGGTHPGHTT DAVAALLAEF LKADLLVVIT NVDGVYTADP
160 170 180 190 200
KKDPTAKKIK KMKPEELLEI VGKGIEKAGS SSVIDPLAAK IIARSGIKTI
210 220
VIGKEDAKDL FRVIKGDHNG TTIEP
Length:225
Mass (Da):24,491
Last modified:June 1, 2002 - v1
Checksum:i510D151A02F8D534
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009950 Genomic DNA. Translation: AAL81531.1.
RefSeqiWP_011012554.1. NC_003413.1.

Genome annotation databases

EnsemblBacteriaiAAL81531; AAL81531; PF1407.
GeneIDi1469283.
KEGGipfu:PF1407.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009950 Genomic DNA. Translation: AAL81531.1.
RefSeqiWP_011012554.1. NC_003413.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2BMUX-ray2.55A/B1-225[»]
2BRIX-ray3.00A/B1-225[»]
2BRXX-ray2.40A/B1-225[»]
2JI5X-ray2.45A/B1-225[»]
ProteinModelPortaliQ8U122.
SMRiQ8U122. Positions 1-225.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi186497.PF1407.

Proteomic databases

PRIDEiQ8U122.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL81531; AAL81531; PF1407.
GeneIDi1469283.
KEGGipfu:PF1407.

Phylogenomic databases

eggNOGiarCOG00858. Archaea.
COG0528. LUCA.
HOGENOMiHOG000047188.
KOiK09903.
OMAiGIHITRA.

Enzyme and pathway databases

UniPathwayiUPA00159; UER00275.
BRENDAi2.7.4.22. 5243.

Miscellaneous databases

EvolutionaryTraceiQ8U122.

Family and domain databases

Gene3Di3.40.1160.10. 1 hit.
HAMAPiMF_01220_A. PyrH_A.
InterProiIPR001048. Asp/Glu/Uridylate_kinase.
IPR011817. Uridylate_kinase.
IPR011818. Uridylate_kinase_arch/spir.
[Graphical view]
PANTHERiPTHR21499:SF23. PTHR21499:SF23. 1 hit.
PfamiPF00696. AA_kinase. 1 hit.
[Graphical view]
PIRSFiPIRSF005650. Uridylate_kin. 1 hit.
SUPFAMiSSF53633. SSF53633. 1 hit.
TIGRFAMsiTIGR02076. pyrH_arch. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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.

Entry informationi

Entry nameiPYRH_PYRFU
AccessioniPrimary (citable) accession number: Q8U122
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 30, 2002
Last sequence update: June 1, 2002
Last modified: November 11, 2015
This is version 85 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

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 one 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.