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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)DescriptionActionsGraphical viewLength
Binding sitei55UMP; via amide nitrogenBy similarity1
Binding sitei56ATP; via amide nitrogenBy similarity1
Binding sitei60ATPBy similarity1
Binding sitei75UMPBy similarity1
Binding sitei163ATPBy similarity1
Binding sitei164ATPBy similarity1
Binding sitei169ATP; via amide nitrogen and carbonyl oxygenBy similarity1
Binding sitei172ATPBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi13 – 16ATPBy similarity4
Nucleotide bindingi136 – 143UMPBy similarity8

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

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)DescriptionActionsGraphical viewLength
ChainiPRO_00001438661 – 239Uridylate kinaseAdd BLAST239

Proteomic databases

PaxDbiP65932.

Interactioni

Subunit structurei

Homohexamer.1 Publication

Protein-protein interaction databases

STRINGi122586.NMB2103.

Structurei

Secondary structure

1239
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi8 – 14Combined sources7
Helixi16 – 20Combined sources5
Beta strandi23 – 26Combined sources4
Helixi29 – 44Combined sources16
Beta strandi48 – 53Combined sources6
Helixi56 – 66Combined sources11
Helixi71 – 95Combined sources25
Beta strandi100 – 106Combined sources7
Beta strandi108 – 111Combined sources4
Helixi117 – 125Combined sources9
Beta strandi129 – 134Combined sources6
Helixi143 – 153Combined sources11
Beta strandi157 – 162Combined sources6
Beta strandi164 – 167Combined sources4
Beta strandi169 – 171Combined sources3
Helixi173 – 175Combined sources3
Beta strandi183 – 186Combined sources4
Helixi187 – 192Combined sources6
Helixi200 – 208Combined sources9
Beta strandi213 – 216Combined sources4
Helixi223 – 229Combined sources7
Beta strandi234 – 238Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1YBDX-ray2.60A/B/C1-239[»]
ProteinModelPortaliP65932.
SMRiP65932.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1YBDX-ray2.60A/B/C1-239[»]
ProteinModelPortaliP65932.
SMRiP65932.
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.
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: November 2, 2016
This is version 80 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.