P55882 (THID_SALTY) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase
EC=2.7.1.49
EC=2.7.4.7

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 names

Name:	thiD
Ordered Locus Names:	STM2146

Organism

Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) [Reference proteome] [HAMAP]

Taxonomic identifier

99287 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Salmonella › Salmonella choleraesuis › Salmonella enterica I › Salmonella typhimurium

Protein attributes

Sequence length	266 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the phosphorylation of hydroxymethylpyrimidine phosphate (HMP-P) to HMP-PP, and of HMP to HMP-P By similarity.
Catalytic activity	ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine = ADP + 4-amino-5-phosphonooxymethyl-2-methylpyrimidine. ATP + 4-amino-2-methyl-5-phosphomethylpyrimidine = ADP + 4-amino-2-methyl-5-diphosphomethylpyrimidine.
Pathway	Cofactor biosynthesis; thiamine diphosphate biosynthesis; 4-amino-2-methyl-5-diphosphomethylpyrimidine from 5-amino-1-(5-phospho-D-ribosyl)imidazole: step 2/3. Cofactor biosynthesis; thiamine diphosphate biosynthesis; 4-amino-2-methyl-5-diphosphomethylpyrimidine from 5-amino-1-(5-phospho-D-ribosyl)imidazole: step 3/3.
Subunit structure	Homodimer. Ref.3
Sequence similarities	Belongs to the ThiD family.

Ontologies

Keywords
Biological process	Thiamine biosynthesis
Ligand	ATP-binding Nucleotide-binding
Molecular function	Kinase Transferase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	thiamine biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW thiamine diphosphate biosynthetic process Inferred from electronic annotation. Source: UniProtKB-UniPathway
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW hydroxymethylpyrimidine kinase activity Inferred from electronic annotation. Source: EC phosphomethylpyrimidine kinase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 266

266

Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase

PRO_0000192026

Sites

Binding site

44

1

Substrate

Experimental info

Sequence conflict

44

1

Q → E in AAB66492. Ref.1

Secondary structure

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266

Helix Strand Turn

Details...

Beta strand

5 – 11

7

Beta strand

16 – 18

3

Helix

19 – 29

11

Beta strand

33 – 45

13

Beta strand

48 – 54

7

Helix

57 – 68

12

Beta strand

74 – 78

5

Helix

84 – 96

13

Beta strand

101 – 105

5

Helix

119 – 128

10

Helix

130 – 132

3

Beta strand

134 – 137

4

Helix

140 – 147

8

Helix

155 – 167

13

Beta strand

171 – 176

6

Beta strand

188 – 190

3

Beta strand

195 – 197

3

Helix

211 – 222

12

Helix

223 – 225

3

Beta strand

226 – 228

3

Helix

229 – 244

16

Helix

245 – 249

5

Beta strand

254 – 256

3

Turn

261 – 265

5

Sequences

	Sequence		Length	Mass (Da)
	P55882 [UniParc]. Last modified January 23, 2002. Version 2. Checksum: F8B94332E1616368	FASTA	266	28,544
	10 20 30 40 50 60 MQRINALTIA GTDPSGGAGI QADLKTFSAL GAYGCSVITA LVAQNTCGVQ SVYRIEPDFV 70 80 90 100 110 120 AAQLDSVFSD VRIDTTKIGM LAETDIVEAV AERLQRHHVR NVVLDTVMLA KSGDPLLSPS 130 140 150 160 170 180 AIETLRVRLL PQVSLITPNL PEAAALLDAP HARTEQEMLA QGRALLAMGC EAVLMKGGHL 190 200 210 220 230 240 EDAQSPDWLF TREGEQRFSA PRVNTKNTHG TGCTLSAALA ALRPRHRSWG ETVNEAKAWL 250 260 SAALAQADTL EVGKGIGPVH HFHAWW

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Identification and characterization of an operon in Salmonella typhimurium involved in thiamine biosynthesis." Petersen L.A., Downs D.M. J. Bacteriol. 179:4894-4900(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: LT2.
[2]	"Complete genome sequence of Salmonella enterica serovar Typhimurium LT2." McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P., Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D., Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E. , Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R., Wilson R.K. Nature 413:852-856(2001) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: LT2 / SGSC1412 / ATCC 700720.
[3]	"Crystal structure of 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase from Salmonella typhimurium at 2.3 A resolution." Cheng G., Bennett E.M., Begley T.P., Ealick S.E. Structure 10:225-235(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH SUBSTRATE, SUBUNIT.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U87940 Genomic DNA. Translation: AAB66492.1.
AE006468 Genomic DNA. Translation: AAL21049.1.

RefSeq

NP_461090.1. NC_003197.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1JXH	X-ray	2.30	A/B	1-266	[»]
1JXI	X-ray	2.64	A/B	1-266	[»]
1LLJ	model	-	A	1-266	[»]

ProteinModelPortal

P55882.

SMR

P55882. Positions 1-266.

ModBase

Search...

Protein-protein interaction databases

STRING

99287.STM2146.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAL21049; AAL21049; STM2146.

GeneID

1253667.

KEGG

stm:STM2146.

PATRIC

32382881. VBISalEnt20916_2271.

Phylogenomic databases

eggNOG

COG0351.

HOGENOM

HOG000225275.

KO

K00941.

OMA

ETCDFGL.

ProtClustDB

PRK06427.

Enzyme and pathway databases

UniPathway

UPA00060; UER00137.
UPA00060; UER00138.

Family and domain databases

InterPro

IPR013749. HMP-P_kinase-1.
IPR004399. HMP-P_kinase-2.
[Graphical view]

Pfam

PF08543. Phos_pyr_kin. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00097. HMP-P_kinase. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P55882.

Entry information

Entry name

THID_SALTY

Accession

Primary (citable) accession number: P55882

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	January 23, 2002
Last modified:	May 1, 2013
This is version 92 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program