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Protein

Uridylate kinase

Gene

pyrH

Organism
Neisseria meningitidis serogroup B (strain MC58)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the reversible phosphorylation of UMP to UDP.1 Publication

Catalytic activityi

ATP + UMP = ADP + UDP.

Enzyme regulationi

Allosterically activated by GTP. Inhibited by UTP.1 Publication

Kineticsi

  1. KM=2.98 mM for ATP (in the absence of GTP)1 Publication
  2. KM=0.83 mM for ATP (in the presence of GTP)1 Publication
  3. KM=8.7 µM for UMP1 Publication
  1. Vmax=35 µmol/min/mg enzyme (in the absence of GTP)1 Publication
  2. Vmax=66 µmol/min/mg enzyme (in the presence of GTP)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 sitei55 – 551UMP; via amide nitrogenBy similarity
Binding sitei56 – 561ATP; via amide nitrogenBy similarity
Binding sitei60 – 601ATPBy similarity
Binding sitei75 – 751UMPBy similarity
Binding sitei163 – 1631ATPBy similarity
Binding sitei164 – 1641ATPBy similarity
Binding sitei169 – 1691ATP; via amide nitrogen and carbonyl oxygenBy similarity
Binding sitei172 – 1721ATPBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi13 – 164ATPBy similarity
Nucleotide bindingi136 – 1438UMPBy 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

BioCyciNMEN122586:GHGG-2168-MONOMER.
BRENDAi2.7.4.22. 3593.
SABIO-RKP65932.
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:NMB2103
OrganismiNeisseria meningitidis serogroup B (strain MC58)
Taxonomic identifieri122586 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaNeisserialesNeisseriaceaeNeisseria
Proteomesi
  • UP000000425 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 – 239239Uridylate kinasePRO_0000143866Add
BLAST

Proteomic databases

PaxDbiP65932.

Interactioni

Subunit structurei

Homohexamer.1 Publication

Protein-protein interaction databases

STRINGi122586.NMB2103.

Structurei

Secondary structure

1
239
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi8 – 147Combined sources
Helixi16 – 205Combined sources
Beta strandi23 – 264Combined sources
Helixi29 – 4416Combined sources
Beta strandi48 – 536Combined sources
Helixi56 – 6611Combined sources
Helixi71 – 9525Combined sources
Beta strandi100 – 1067Combined sources
Beta strandi108 – 1114Combined sources
Helixi117 – 1259Combined sources
Beta strandi129 – 1346Combined sources
Helixi143 – 15311Combined sources
Beta strandi157 – 1626Combined sources
Beta strandi164 – 1674Combined sources
Beta strandi169 – 1713Combined sources
Helixi173 – 1753Combined sources
Beta strandi183 – 1864Combined sources
Helixi187 – 1926Combined sources
Helixi200 – 2089Combined sources
Beta strandi213 – 2164Combined sources
Helixi223 – 2297Combined sources
Beta strandi234 – 2385Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1YBDX-ray2.60A/B/C1-239[»]
ProteinModelPortaliP65932.
SMRiP65932. Positions 4-239.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP65932.

Family & Domainsi

Sequence similaritiesi

Belongs to the UMP kinase family.Curated

Phylogenomic databases

eggNOGiENOG4105C41. Bacteria.
COG0528. LUCA.
HOGENOMiHOG000047187.
KOiK09903.
OMAiRSRADYM.
OrthoDBiPOG091H02JZ.

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.

P65932-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTQQIKYKRV LLKLSGESLM GSDPFGINHD TIVQTVGEIA EVVKMGVQVG
60 70 80 90 100
IVVGGGNIFR GVSAQAGSMD RATADYMGMM ATVMNALALK DAFETLGIKA
110 120 130 140 150
RVQSALSMQQ IAETYARPKA IQYLEEGKVV IFAAGTGNPF FTTDTAAALR
160 170 180 190 200
GAEMNCDVML KATNVDGVYT ADPKKDPSAT RYETITFDEA LLKNLKVMDA
210 220 230
TAFALCRERK LNIVVFGIAK EGSLKRVITG EDEGTLVHC
Length:239
Mass (Da):25,700
Last modified:October 11, 2004 - v1
Checksum:iCB08FD7E1AFBC5FE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE002098 Genomic DNA. Translation: AAF42420.1.
PIRiH81006.
RefSeqiNP_275091.1. NC_003112.2.
WP_002215090.1. NC_003112.2.

Genome annotation databases

EnsemblBacteriaiAAF42420; AAF42420; NMB2103.
GeneIDi903933.
KEGGinme:NMB2103.
PATRICi20360376. VBINeiMen85645_2685.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE002098 Genomic DNA. Translation: AAF42420.1.
PIRiH81006.
RefSeqiNP_275091.1. NC_003112.2.
WP_002215090.1. NC_003112.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1YBDX-ray2.60A/B/C1-239[»]
ProteinModelPortaliP65932.
SMRiP65932. Positions 4-239.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi122586.NMB2103.

Proteomic databases

PaxDbiP65932.

Protocols and materials databases

DNASUi903933.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAF42420; AAF42420; NMB2103.
GeneIDi903933.
KEGGinme:NMB2103.
PATRICi20360376. VBINeiMen85645_2685.

Phylogenomic databases

eggNOGiENOG4105C41. Bacteria.
COG0528. LUCA.
HOGENOMiHOG000047187.
KOiK09903.
OMAiRSRADYM.
OrthoDBiPOG091H02JZ.

Enzyme and pathway databases

UniPathwayiUPA00159; UER00275.
BioCyciNMEN122586:GHGG-2168-MONOMER.
BRENDAi2.7.4.22. 3593.
SABIO-RKP65932.

Miscellaneous databases

EvolutionaryTraceiP65932.

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_NEIMB
AccessioniPrimary (citable) accession number: P65932
Secondary accession number(s): Q9JQT5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 11, 2004
Last sequence update: October 11, 2004
Last modified: September 7, 2016
This is version 78 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, Allosteric enzyme, 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.