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Protein

Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase

Gene

thiD

Organism
Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Catalyzes the phosphorylation of hydroxymethylpyrimidine phosphate (HMP-P) to HMP-PP, and of HMP to HMP-P.By similarity

Catalytic activityi

ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine = ADP + 4-amino-2-methyl-5-(phosphomethyl)pyrimidine.By similarity
ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine = ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine.By similarity

Pathwayi: thiamine diphosphate biosynthesis

This protein is involved in step 2 and 3 of the subpathway that synthesizes 4-amino-2-methyl-5-diphosphomethylpyrimidine from 5-amino-1-(5-phospho-D-ribosyl)imidazole.
Proteins known to be involved in the 3 steps of the subpathway in this organism are:
  1. no protein annotated in this organism
  2. Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase (thiD)
  3. Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase (thiD)
This subpathway is part of the pathway thiamine diphosphate biosynthesis, which is itself part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes 4-amino-2-methyl-5-diphosphomethylpyrimidine from 5-amino-1-(5-phospho-D-ribosyl)imidazole, the pathway thiamine diphosphate biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei43SubstrateBy similarity1

GO - Molecular functioni

GO - Biological processi

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Biological processi

Thiamine biosynthesis

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

UniPathwayiUPA00060; UER00137.
UPA00060; UER00138.

Names & Taxonomyi

Protein namesi
Recommended name:
Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase (EC:2.7.1.49By similarity, EC:2.7.4.7By similarity)
Alternative name(s):
Hydroxymethylpyrimidine kinase
Short name:
HMP kinase
Hydroxymethylpyrimidine phosphate kinase
Short name:
HMP-P kinase
Short name:
HMP-phosphate kinase
Short name:
HMPP kinase
Gene namesi
Name:thiD
Ordered Locus Names:RB1087
ORF Names:SMb20962
Encoded oniPlasmid pSymB (megaplasmid 2)0 Publication
OrganismiRhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)
Taxonomic identifieri266834 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeSinorhizobium/Ensifer groupSinorhizobium
Proteomesi
  • UP000001976 Componenti: Plasmid pSymB

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001920251 – 266Hydroxymethylpyrimidine/phosphomethylpyrimidine kinaseAdd BLAST266

Structurei

3D structure databases

ProteinModelPortaliP56904.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the ThiD family.Curated

Phylogenomic databases

KOiK00941.
OMAiFAFHCVH.

Family and domain databases

CDDicd01169. HMPP_kinase. 1 hit.
Gene3Di3.40.1190.20. 1 hit.
InterProiIPR004399. HMP/HMP-P_kinase.
IPR013749. PM/HMP-P_kinase-1.
IPR029056. Ribokinase-like.
[Graphical view]
PfamiPF08543. Phos_pyr_kin. 1 hit.
[Graphical view]
SUPFAMiSSF53613. SSF53613. 1 hit.
TIGRFAMsiTIGR00097. HMP-P_kinase. 1 hit.

Sequencei

Sequence statusi: Complete.

P56904-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTAIALSIAG SDSGGGAGIQ ADLKTFSALG VYGASVITAI TAQNTRGVTA
60 70 80 90 100
VEDVSAEIVS AQMDAVFSDL DVKAVKIGMV SRRETIAAIA DGLRRFGKRA
110 120 130 140 150
VVDPVMVATS GDALLRPDAV AALIEELLPL ALVVTPNLAE AALMTGRAIA
160 170 180 190 200
GDEAEMARQA EAIMRTGAHA VLVKGGHLKG QEATDLFFDG DTLVRLPAGR
210 220 230 240 250
IETRNDHGTG CTLSAAIAAG LAKGVPLIEA VSAAKAYLHA AISAADRLEI
260
GQGRGPVHHF HRWWKD
Length:266
Mass (Da):27,423
Last modified:November 2, 2001 - v2
Checksum:i803D0C58EB9A1830
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti98 – 99KR → RL in AAD46983 (Ref. 1) Curated2
Sequence conflicti115L → F in AAD46983 (Ref. 1) Curated1
Sequence conflicti134V → A in AAD46983 (Ref. 1) Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF070520 Genomic DNA. Translation: AAD46983.1.
AL591985 Genomic DNA. Translation: CAC49487.1.
Z22636 Genomic DNA. Translation: CAA80350.1. Sequence problems.
PIRiG95977.
S78110.
RefSeqiNP_437627.1. NC_003078.1.
WP_010975923.1. NC_003078.1.

Genome annotation databases

EnsemblBacteriaiCAC49487; CAC49487; SM_b20962.
GeneIDi1237418.
KEGGisme:SM_b20962.
PATRICi23638592. VBISinMel96828_6017.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF070520 Genomic DNA. Translation: AAD46983.1.
AL591985 Genomic DNA. Translation: CAC49487.1.
Z22636 Genomic DNA. Translation: CAA80350.1. Sequence problems.
PIRiG95977.
S78110.
RefSeqiNP_437627.1. NC_003078.1.
WP_010975923.1. NC_003078.1.

3D structure databases

ProteinModelPortaliP56904.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAC49487; CAC49487; SM_b20962.
GeneIDi1237418.
KEGGisme:SM_b20962.
PATRICi23638592. VBISinMel96828_6017.

Phylogenomic databases

KOiK00941.
OMAiFAFHCVH.

Enzyme and pathway databases

UniPathwayiUPA00060; UER00137.
UPA00060; UER00138.

Family and domain databases

CDDicd01169. HMPP_kinase. 1 hit.
Gene3Di3.40.1190.20. 1 hit.
InterProiIPR004399. HMP/HMP-P_kinase.
IPR013749. PM/HMP-P_kinase-1.
IPR029056. Ribokinase-like.
[Graphical view]
PfamiPF08543. Phos_pyr_kin. 1 hit.
[Graphical view]
SUPFAMiSSF53613. SSF53613. 1 hit.
TIGRFAMsiTIGR00097. HMP-P_kinase. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiTHID_RHIME
AccessioniPrimary (citable) accession number: P56904
Secondary accession number(s): Q52914
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: November 2, 2001
Last modified: November 2, 2016
This is version 95 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Plasmid, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.