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Protein

Uridylate kinase

Gene

pyrH

Organism
Ureaplasma parvum serovar 3 (strain ATCC 700970)
Status
Reviewed-Annotation score: Annotation score: 4 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. Is also able to phosphorylate dUMP.2 Publications

Catalytic activityi

ATP + UMP = ADP + UDP.

Enzyme regulationi

Unlike other bacteria, is not activated by GTP. UTP is a competitive inhibitor against UMP and a non-competitive inhibitor toward ATP.1 Publication

Kineticsi

Positive cooperativity is observed with ATP as variable substrate, but it is abolished in the presence of UTP.

  1. KM=214 µM for UMP1 Publication
  1. Vmax=262 µmol/min/mg enzyme1 Publication

pH dependencei

Optimum pH is 6.8.1 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 sitei50 – 501UMP; via amide nitrogenBy similarity
Binding sitei51 – 511ATP; via amide nitrogenBy similarity
Binding sitei55 – 551ATPBy similarity
Binding sitei70 – 701UMPBy similarity
Binding sitei159 – 1591ATPBy similarity
Binding sitei165 – 1651ATP; via amide nitrogen and carbonyl oxygenBy similarity
Binding sitei168 – 1681ATPBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi9 – 124ATPBy similarity
Nucleotide bindingi131 – 1388UMPBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Biological processi

Pyrimidine biosynthesis

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciUPAR273119:GHVP-544-MONOMER.
BRENDAi2.7.4.22. 9209.
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:UU513
OrganismiUreaplasma parvum serovar 3 (strain ATCC 700970)
Taxonomic identifieri273119 [NCBI]
Taxonomic lineageiBacteriaTenericutesMollicutesMycoplasmataceaeUreaplasma
Proteomesi
  • UP000000423 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi133 – 1331F → N or A: Still no activation by GTP. Exhibits negative cooperativity with UMP. Marked decrease in activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 235235Uridylate kinasePRO_0000143902Add
BLAST

Interactioni

Subunit structurei

Homohexamer; trimer of dimers.1 Publication

Protein-protein interaction databases

STRINGi273119.UU513.

Structurei

Secondary structure

1
235
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 107Combined sources
Helixi12 – 154Combined sources
Helixi25 – 3814Combined sources
Turni39 – 413Combined sources
Beta strandi42 – 487Combined sources
Turni51 – 533Combined sources
Helixi56 – 616Combined sources
Helixi66 – 8924Combined sources
Turni90 – 923Combined sources
Beta strandi95 – 1017Combined sources
Turni104 – 1063Combined sources
Helixi112 – 1209Combined sources
Beta strandi124 – 1296Combined sources
Beta strandi132 – 1354Combined sources
Helixi138 – 14912Combined sources
Beta strandi152 – 1609Combined sources
Turni169 – 1713Combined sources
Beta strandi178 – 1825Combined sources
Helixi183 – 1897Combined sources
Helixi196 – 2049Combined sources
Beta strandi208 – 2169Combined sources
Helixi219 – 2246Combined sources
Beta strandi231 – 2344Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2VA1X-ray2.50A/B/C/D/E/F1-235[»]
ProteinModelPortaliQ9PPX6.
SMRiQ9PPX6. Positions 1-235.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9PPX6.

Family & Domainsi

Sequence similaritiesi

Belongs to the UMP kinase family.Curated

Phylogenomic databases

eggNOGiENOG4105C41. Bacteria.
COG0528. LUCA.
HOGENOMiHOG000047187.
KOiK09903.
OMAiIMEYANI.

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.

Q9PPX6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRKQRIVIKI SGACLKQNDS SIIDFIKIND LAEQIEKISK KYIVSIVLGG
60 70 80 90 100
GNIWRGSIAK ELDMDRNLAD NMGMMATIIN GLALENALNH LNVNTIVLSA
110 120 130 140 150
IKCDKLVHES SANNIKKAIE KEQVMIFVAG TGFPYFTTDS CAAIRAAETE
160 170 180 190 200
SSIILMGKNG VDGVYDSDPK INPNAQFYEH ITFNMALTQN LKVMDATALA
210 220 230
LCQENNINLL VFNIDKPNAI VDVLEKKNKY TIVSK
Length:235
Mass (Da):25,924
Last modified:October 1, 2000 - v1
Checksum:iCAF39D32C3DFCE2D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF222894 Genomic DNA. Translation: AAF30926.1.
RefSeqiWP_006688575.1. NC_002162.1.

Genome annotation databases

EnsemblBacteriaiAAF30926; AAF30926; UU513.
GeneIDi875982.
KEGGiuur:UU513.
PATRICi20534641. VBIUrePar45146_0533.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF222894 Genomic DNA. Translation: AAF30926.1.
RefSeqiWP_006688575.1. NC_002162.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2VA1X-ray2.50A/B/C/D/E/F1-235[»]
ProteinModelPortaliQ9PPX6.
SMRiQ9PPX6. Positions 1-235.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi273119.UU513.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAF30926; AAF30926; UU513.
GeneIDi875982.
KEGGiuur:UU513.
PATRICi20534641. VBIUrePar45146_0533.

Phylogenomic databases

eggNOGiENOG4105C41. Bacteria.
COG0528. LUCA.
HOGENOMiHOG000047187.
KOiK09903.
OMAiIMEYANI.

Enzyme and pathway databases

UniPathwayiUPA00159; UER00275.
BioCyciUPAR273119:GHVP-544-MONOMER.
BRENDAi2.7.4.22. 9209.

Miscellaneous databases

EvolutionaryTraceiQ9PPX6.

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_UREPA
AccessioniPrimary (citable) accession number: Q9PPX6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 30, 2002
Last sequence update: October 1, 2000
Last modified: September 7, 2016
This is version 88 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.