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Protein

Uridylate kinase

Gene

pyrH

Organism
Escherichia coli (strain K12)
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

Allosterically activated by GTP. Competitively inhibited by magnesium-free UTP. Magnesium-bound UTP is unable to inhibit enzyme activity.2 Publications

Kineticsi

  1. KM=120 µM for ATP1 Publication
  2. KM=50 µM for UMP1 Publication
  1. Vmax=96 µmol/min/mg enzyme1 Publication

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
Binding sitei57 – 571UMP; via amide nitrogen1 Publication
Binding sitei58 – 581ATP; via amide nitrogenBy similarity
Binding sitei62 – 621ATPBy similarity
Binding sitei77 – 771UMP1 Publication
Binding sitei165 – 1651ATPBy similarity
Binding sitei171 – 1711ATP; via amide nitrogen and carbonyl oxygenBy similarity
Binding sitei174 – 1741ATPBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi15 – 184ATPBy similarity
Nucleotide bindingi138 – 1458UMP1 Publication

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • identical protein binding Source: EcoCyc
  • UMP kinase activity Source: EcoCyc

GO - Biological processi

  • 'de novo' CTP biosynthetic process Source: UniProtKB-UniPathway
  • pyrimidine nucleotide biosynthetic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Biological processi

Pyrimidine biosynthesis

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:UMPKI-MONOMER.
ECOL316407:JW0166-MONOMER.
MetaCyc:UMPKI-MONOMER.
BRENDAi2.7.4.22. 2026.
SABIO-RKP0A7E9.
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
Synonyms:smbA
Ordered Locus Names:b0171, JW0166
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11539. pyrH.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi62 – 621R → H: Loss of activation by GTP and decreased affinity for UTP. 1 Publication
Mutagenesisi77 – 771D → N: Loss of activation by GTP and decreased affinity for UTP. 1 Publication
Mutagenesisi138 – 1381T → A: Loss of activation by GTP. Moderate loss of sensitivity to UTP inhibition. 4-fold and 2-fold decrease in affinity for UMP and ATP, respectively. 1 Publication
Mutagenesisi140 – 1401N → A: Loss of activation by GTP. Moderate loss of sensitivity to UTP inhibition. 1 Publication
Mutagenesisi146 – 1461D → N: Drastically reduced activity. 1 Publication
Mutagenesisi159 – 1591D → N: Increased solubility at neutral pH. Nearly no change in kinetic properties and stability. 1 Publication
Mutagenesisi174 – 1741D → N: Reduced UMP-binding affinity. 1 Publication
Mutagenesisi201 – 2011D → N: Loss of activation by GTP. 2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved1 Publication
Chaini2 – 241240Uridylate kinasePRO_0000143842Add
BLAST

Proteomic databases

EPDiP0A7E9.
PaxDbiP0A7E9.
PRIDEiP0A7E9.

Interactioni

Subunit structurei

Homohexamer.2 Publications

GO - Molecular functioni

  • identical protein binding Source: EcoCyc

Protein-protein interaction databases

BioGridi4262225. 6 interactions.
DIPiDIP-31830N.
IntActiP0A7E9. 54 interactions.
MINTiMINT-1222953.
STRINGi511145.b0171.

Structurei

Secondary structure

1
241
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi10 – 167Combined sources
Helixi18 – 214Combined sources
Beta strandi26 – 283Combined sources
Helixi31 – 4616Combined sources
Beta strandi50 – 556Combined sources
Turni58 – 603Combined sources
Helixi63 – 686Combined sources
Helixi73 – 9725Combined sources
Beta strandi102 – 1087Combined sources
Turni111 – 1133Combined sources
Beta strandi114 – 1163Combined sources
Helixi119 – 1279Combined sources
Beta strandi131 – 1366Combined sources
Beta strandi139 – 1424Combined sources
Helixi145 – 15511Combined sources
Beta strandi159 – 16911Combined sources
Beta strandi171 – 1733Combined sources
Turni175 – 1773Combined sources
Beta strandi185 – 1884Combined sources
Helixi189 – 1946Combined sources
Helixi202 – 2109Combined sources
Beta strandi215 – 2195Combined sources
Helixi225 – 2306Combined sources
Beta strandi236 – 2405Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2BNDX-ray2.60A/B1-241[»]
2BNEX-ray2.30A/B1-241[»]
2BNFX-ray2.45A/B1-241[»]
2V4YX-ray2.80A/B/C/D/E/F1-241[»]
ProteinModelPortaliP0A7E9.
SMRiP0A7E9. Positions 3-241.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A7E9.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni23 – 286Involved in allosteric activation by GTPSequence analysis

Sequence similaritiesi

Belongs to the UMP kinase family.Curated

Phylogenomic databases

eggNOGiENOG4105C41. Bacteria.
COG0528. LUCA.
HOGENOMiHOG000047187.
InParanoidiP0A7E9.
KOiK09903.
OMAiKGLKVMD.
PhylomeDBiP0A7E9.

Family and domain databases

Gene3Di3.40.1160.10. 1 hit.
HAMAPiMF_01220_B. PyrH_B. 1 hit.
InterProiIPR001048. Asp/Glu/Uridylate_kinase.
IPR011817. Uridylate_kinase.
IPR015963. Uridylate_kinase_bac.
[Graphical view]
PANTHERiPTHR21499:SF23. PTHR21499:SF23. 1 hit.
PfamiPF00696. AA_kinase. 1 hit.
[Graphical view]
PIRSFiPIRSF005650. Uridylate_kin. 1 hit.
SUPFAMiSSF53633. SSF53633. 1 hit.
TIGRFAMsiTIGR02075. pyrH_bact. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0A7E9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MATNAKPVYK RILLKLSGEA LQGTEGFGID ASILDRMAQE IKELVELGIQ
60 70 80 90 100
VGVVIGGGNL FRGAGLAKAG MNRVVGDHMG MLATVMNGLA MRDALHRAYV
110 120 130 140 150
NARLMSAIPL NGVCDSYSWA EAISLLRNNR VVILSAGTGN PFFTTDSAAC
160 170 180 190 200
LRGIEIEADV VLKATKVDGV FTADPAKDPT ATMYEQLTYS EVLEKELKVM
210 220 230 240
DLAAFTLARD HKLPIRVFNM NKPGALRRVV MGEKEGTLIT E
Length:241
Mass (Da):25,970
Last modified:January 23, 2007 - v2
Checksum:i82EFA75F7226E201
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti64 – 696AGLAKA → RWSGET in CAA55388 (Ref. 1) Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti62 – 621R → H in Smba9.
Natural varianti201 – 2011D → N in Smba2.

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X78809 Genomic DNA. Translation: CAA55388.1.
D13334 Genomic DNA. Translation: BAA02598.1.
U70214 Genomic DNA. Translation: AAB08600.1.
U00096 Genomic DNA. Translation: AAC73282.1.
AP009048 Genomic DNA. Translation: BAB96747.1.
PIRiB45269.
RefSeqiNP_414713.1. NC_000913.3.
WP_000224573.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73282; AAC73282; b0171.
BAB96747; BAB96747; BAB96747.
GeneIDi944989.
KEGGiecj:JW0166.
eco:b0171.
PATRICi32115451. VBIEscCol129921_0177.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X78809 Genomic DNA. Translation: CAA55388.1.
D13334 Genomic DNA. Translation: BAA02598.1.
U70214 Genomic DNA. Translation: AAB08600.1.
U00096 Genomic DNA. Translation: AAC73282.1.
AP009048 Genomic DNA. Translation: BAB96747.1.
PIRiB45269.
RefSeqiNP_414713.1. NC_000913.3.
WP_000224573.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2BNDX-ray2.60A/B1-241[»]
2BNEX-ray2.30A/B1-241[»]
2BNFX-ray2.45A/B1-241[»]
2V4YX-ray2.80A/B/C/D/E/F1-241[»]
ProteinModelPortaliP0A7E9.
SMRiP0A7E9. Positions 3-241.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262225. 6 interactions.
DIPiDIP-31830N.
IntActiP0A7E9. 54 interactions.
MINTiMINT-1222953.
STRINGi511145.b0171.

Proteomic databases

EPDiP0A7E9.
PaxDbiP0A7E9.
PRIDEiP0A7E9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73282; AAC73282; b0171.
BAB96747; BAB96747; BAB96747.
GeneIDi944989.
KEGGiecj:JW0166.
eco:b0171.
PATRICi32115451. VBIEscCol129921_0177.

Organism-specific databases

EchoBASEiEB1501.
EcoGeneiEG11539. pyrH.

Phylogenomic databases

eggNOGiENOG4105C41. Bacteria.
COG0528. LUCA.
HOGENOMiHOG000047187.
InParanoidiP0A7E9.
KOiK09903.
OMAiKGLKVMD.
PhylomeDBiP0A7E9.

Enzyme and pathway databases

UniPathwayiUPA00159; UER00275.
BioCyciEcoCyc:UMPKI-MONOMER.
ECOL316407:JW0166-MONOMER.
MetaCyc:UMPKI-MONOMER.
BRENDAi2.7.4.22. 2026.
SABIO-RKP0A7E9.

Miscellaneous databases

EvolutionaryTraceiP0A7E9.
PROiP0A7E9.

Family and domain databases

Gene3Di3.40.1160.10. 1 hit.
HAMAPiMF_01220_B. PyrH_B. 1 hit.
InterProiIPR001048. Asp/Glu/Uridylate_kinase.
IPR011817. Uridylate_kinase.
IPR015963. Uridylate_kinase_bac.
[Graphical view]
PANTHERiPTHR21499:SF23. PTHR21499:SF23. 1 hit.
PfamiPF00696. AA_kinase. 1 hit.
[Graphical view]
PIRSFiPIRSF005650. Uridylate_kin. 1 hit.
SUPFAMiSSF53633. SSF53633. 1 hit.
TIGRFAMsiTIGR02075. pyrH_bact. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiPYRH_ECOLI
AccessioniPrimary (citable) accession number: P0A7E9
Secondary accession number(s): P29464
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: January 23, 2007
Last modified: September 7, 2016
This is version 101 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The peripheral distribution of PyrH is related most probably to its role in the synthesis of membrane sugar components.

Keywords - Technical termi

3D-structure, Allosteric enzyme, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.