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Protein

Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase

Gene

thiD

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

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 sitei44Substrate1 Publication1

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:STM2146
OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Taxonomic identifieri99287 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
Proteomesi
  • UP000001014 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001920261 – 266Hydroxymethylpyrimidine/phosphomethylpyrimidine kinaseAdd BLAST266

Proteomic databases

PaxDbiP55882.
PRIDEiP55882.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi99287.STM2146.

Structurei

Secondary structure

1266
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi5 – 11Combined sources7
Beta strandi16 – 18Combined sources3
Helixi19 – 29Combined sources11
Beta strandi33 – 45Combined sources13
Beta strandi48 – 54Combined sources7
Helixi57 – 68Combined sources12
Beta strandi74 – 78Combined sources5
Helixi84 – 96Combined sources13
Beta strandi101 – 105Combined sources5
Helixi119 – 128Combined sources10
Helixi130 – 132Combined sources3
Beta strandi134 – 137Combined sources4
Helixi140 – 147Combined sources8
Helixi155 – 167Combined sources13
Beta strandi171 – 176Combined sources6
Beta strandi188 – 190Combined sources3
Beta strandi195 – 197Combined sources3
Helixi211 – 222Combined sources12
Helixi223 – 225Combined sources3
Beta strandi226 – 228Combined sources3
Helixi229 – 244Combined sources16
Helixi245 – 249Combined sources5
Beta strandi254 – 256Combined sources3
Turni261 – 265Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1JXHX-ray2.30A/B1-266[»]
1JXIX-ray2.64A/B1-266[»]
1LLJmodel-A1-266[»]
ProteinModelPortaliP55882.
SMRiP55882.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP55882.

Family & Domainsi

Sequence similaritiesi

Belongs to the ThiD family.Curated

Phylogenomic databases

eggNOGiENOG4105DWF. Bacteria.
COG0351. LUCA.
HOGENOMiHOG000225275.
KOiK00941.
OMAiFAFHCVH.
PhylomeDBiP55882.

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.

P55882-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQRINALTIA GTDPSGGAGI QADLKTFSAL GAYGCSVITA LVAQNTCGVQ
60 70 80 90 100
SVYRIEPDFV AAQLDSVFSD VRIDTTKIGM LAETDIVEAV AERLQRHHVR
110 120 130 140 150
NVVLDTVMLA KSGDPLLSPS AIETLRVRLL PQVSLITPNL PEAAALLDAP
160 170 180 190 200
HARTEQEMLA QGRALLAMGC EAVLMKGGHL EDAQSPDWLF TREGEQRFSA
210 220 230 240 250
PRVNTKNTHG TGCTLSAALA ALRPRHRSWG ETVNEAKAWL SAALAQADTL
260
EVGKGIGPVH HFHAWW
Length:266
Mass (Da):28,544
Last modified:January 23, 2002 - v2
Checksum:iF8B94332E1616368
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti44Q → E in AAB66492 (PubMed:9244280).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U87940 Genomic DNA. Translation: AAB66492.1.
AE006468 Genomic DNA. Translation: AAL21049.1.
RefSeqiNP_461090.1. NC_003197.1.
WP_001188957.1. NC_003197.1.

Genome annotation databases

EnsemblBacteriaiAAL21049; AAL21049; STM2146.
GeneIDi1253667.
KEGGistm:STM2146.
PATRICi32382881. VBISalEnt20916_2271.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U87940 Genomic DNA. Translation: AAB66492.1.
AE006468 Genomic DNA. Translation: AAL21049.1.
RefSeqiNP_461090.1. NC_003197.1.
WP_001188957.1. NC_003197.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1JXHX-ray2.30A/B1-266[»]
1JXIX-ray2.64A/B1-266[»]
1LLJmodel-A1-266[»]
ProteinModelPortaliP55882.
SMRiP55882.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi99287.STM2146.

Proteomic databases

PaxDbiP55882.
PRIDEiP55882.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL21049; AAL21049; STM2146.
GeneIDi1253667.
KEGGistm:STM2146.
PATRICi32382881. VBISalEnt20916_2271.

Phylogenomic databases

eggNOGiENOG4105DWF. Bacteria.
COG0351. LUCA.
HOGENOMiHOG000225275.
KOiK00941.
OMAiFAFHCVH.
PhylomeDBiP55882.

Enzyme and pathway databases

UniPathwayiUPA00060; UER00137.
UPA00060; UER00138.

Miscellaneous databases

EvolutionaryTraceiP55882.

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_SALTY
AccessioniPrimary (citable) accession number: P55882
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: January 23, 2002
Last modified: November 2, 2016
This is version 111 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

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.