P26393 (RMLA_SALTY) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Glucose-1-phosphate thymidylyltransferase
EC=2.7.7.24

Alternative name(s):
dTDP-glucose pyrophosphorylase
Short name=Ep
dTDP-glucose synthase

Gene names

Name:	rmlA
Synonyms:	rfbA
Ordered Locus Names:	STM2095

Organism

Salmonella typhimurium

Taxonomic identifier

90371 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Salmonella

Protein attributes

Sequence length	292 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the formation of dTDP-glucose, from dTTP and glucose 1-phosphate, as well as its pyrophosphorolysis. Is also able to convert non natural substrates such as a wide array of alpha-D-hexopyranosyl, deoxy-alpha-D-glucopyranosyl, aminodeoxy-alpha-D-hexopyranosyl and acetamidodeoxy-alpha-D-hexopyranosyl phosphates to their corresponding dTDP- and UDP-nucleotide sugars. Ref.3
Catalytic activity	dTTP + alpha-D-glucose 1-phosphate = diphosphate + dTDP-glucose.
Cofactor	Binds 1 magnesium ion per subunit Probable.
Pathway	Carbohydrate biosynthesis; dTDP-L-rhamnose biosynthesis. Bacterial outer membrane biogenesis; LPS O-antigen biosynthesis.
Subunit structure	Homotetramer.
Sequence similarities	Belongs to the glucose-1-phosphate thymidylyltransferase family.
Caution	The position of the magnesium ion observed in the crystallographic structure is different from that observed in the structure of E.coli rmlA2 (rffH) and does not seem to correspond to the binding site for the catalytically essential magnesium ion. Therefore, we choose to propagate in the feature lines the positions found in the E.coli structure.
Biophysicochemical properties	Kinetic parameters: KM=0.7 mM for dTTP KM=0.3 mM for G1P

Ontologies

Keywords
Biological process	Lipopolysaccharide biosynthesis
Ligand	Magnesium Metal-binding
Molecular function	Nucleotidyltransferase Transferase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	extracellular polysaccharide biosynthetic process Inferred from direct assay Ref.3. Source: UniProtKB lipopolysaccharide biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	glucose-1-phosphate thymidylyltransferase activity Inferred from direct assay Ref.3. Source: UniProtKB magnesium ion binding Inferred from direct assay Ref.4. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 292

292

Glucose-1-phosphate thymidylyltransferase

PRO_0000207995

Sites

Metal binding

111

1

Magnesium By similarity

Metal binding

226

1

Magnesium By similarity

Experimental info

Mutagenesis

201

1

T → A: Two-fold increase in the conversion of 2-acetamido-2-deoxy-alpha-D-glucopyranosyl phosphate. Ref.4

Mutagenesis

224

1

W → H: Is able to convert both 6-acetamido-6-deoxy-alpha-D-glucopyranosyl phosphate and alpha-D-glucopyranuronic acid 1-(dihydrogen phosphate), which are not accepted by the wild-type. Ref.4

Secondary structure

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292

Helix Strand Turn

Details...

Beta strand

5 – 9

5

Helix

15 – 17

3

Turn

18 – 22

5

Helix

26 – 28

3

Beta strand

29 – 35

7

Helix

38 – 46

9

Beta strand

51 – 56

6

Turn

58 – 60

3

Helix

61 – 68

8

Helix

72 – 74

3

Beta strand

77 – 82

6

Helix

89 – 91

3

Helix

92 – 95

4

Helix

97 – 100

4

Beta strand

105 – 109

5

Beta strand

112 – 115

4

Helix

119 – 128

10

Beta strand

130 – 139

10

Helix

143 – 145

3

Beta strand

146 – 151

6

Beta strand

157 – 163

7

Beta strand

168 – 179

12

Helix

183 – 189

7

Helix

200 – 209

10

Beta strand

213 – 217

5

Beta strand

222 – 226

5

Helix

230 – 247

18

Helix

254 – 260

7

Helix

266 – 273

8

Helix

274 – 276

3

Helix

280 – 288

9

Sequences

	Sequence		Length	Mass (Da)
	P26393 [UniParc]. Last modified August 1, 1992. Version 1. Checksum: 11065BA9DF2B0268	FASTA	292	32,453
	10 20 30 40 50 60 MKTRKGIILA GGSGTRLYPV TMAVSKQLLP IYDKPMIYYP LSTLMLAGIR DILIISTPQD 70 80 90 100 110 120 TPRFQQLLGD GSQWGLNLQY KVQPSPDGLA QAFIIGEEFI GHDDCALVLG DNIFYGHDLP 130 140 150 160 170 180 KLMEAAVNKE SGATVFAYHV NDPERYGVVE FDQKGTAVSL EEKPLQPKSN YAVTGLYFYD 190 200 210 220 230 240 NSVVEMAKNL KPSARGELEI TDINRIYMEQ GRLSVAMMGR GYAWLDTGTH QSLIEASNFI 250 260 270 280 290 ATIEERQGLK VSCPEEIAFR KNFINAQQVI ELAGPLSKND YGKYLLKMVK GL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Structure and sequence of the rfb (O antigen) gene cluster of Salmonella serovar typhimurium (strain LT2)." Jiang X.-M., Neal B., Santiago F., Lee S.J., Romana L.K., Reeves P.R. Mol. Microbiol. 5:695-713(1991) [PubMed: 1710759] [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: 11677609] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: LT2 / SGSC1412 / ATCC 700720.
[3]	"Purification, characterization and HPLC assay of Salmonella glucose-1-phosphate thymidylyltransferase from the cloned rfbA gene." Lindquist L., Kaiser R., Reeves P.R., Lindberg A.A. Eur. J. Biochem. 211:763-770(1993) [PubMed: 8382158] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-22, FUNCTION. Strain: LT2.
[4]	"Structure, mechanism and engineering of a nucleotidylyltransferase as a first step toward glycorandomization." Barton W.A., Lesniak J., Biggins J.B., Jeffrey P.D., Jiang J., Rajashankar K.R., Thorson J.S., Nikolov D.B. Nat. Struct. Biol. 8:545-551(2001) [PubMed: 11373625] [Abstract] Cited for: CHARACTERIZATION, MUTAGENESIS OF THR-201 AND TRP-224, X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF COMPLEXES WITH UDP-GLC AND DTTP. Strain: LT2.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X56793 Genomic DNA. Translation: CAA40117.1.
AE006468 Genomic DNA. Translation: AAL20999.1.

PIR

S15301.

RefSeq

NP_461040.1. NC_003197.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1IIM	X-ray	2.10	A/B	1-292	[»]
1IIN	X-ray	2.10	A/B/C/D	1-292	[»]
1MP3	X-ray	2.20	A/B	1-292	[»]
1MP4	X-ray	2.20	A/B	1-292	[»]
1MP5	X-ray	2.75	A	1-292	[»]
3PKP	X-ray	2.60	A/B/C/D/I/J/K/L	1-292	[»]
3PKQ	X-ray	2.40	A/B/C/D	1-292	[»]

ProteinModelPortal

P26393.

SMR

P26393. Positions 1-289.

ModBase

Search...

Proteomic databases

PRIDE

P26393.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

1253616.

GenomeReviews

Gene locus STM2095 in contig AE006468_GR.

KEGG

stm:STM2095.

NMPDR

fig|99287.1.peg.2020.

PATRIC

32382773. VBISalEnt20916_2217.

Phylogenomic databases

HOGENOM

HBG688195.

OMA

YRAGWID.

ProtClustDB

PRK15480.

Enzyme and pathway databases

BioCyc

STYP99287:STM2095-MONOMER.

Family and domain databases

InterPro

IPR005907. G1P_thy_trans_s.
IPR005835. NTP_transferase.
[Graphical view]

KO

K00973.

PANTHER

PTHR22572:SF13. PTHR22572:SF13. 1 hit.

Pfam

PF00483. NTP_transferase. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01207. RmlA. 1 hit.

ProtoNet

Search...

Entry information

Entry name

RMLA_SALTY

Accession

Primary (citable) accession number: P26393

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1992
Last sequence update:	August 1, 1992
Last modified:	January 25, 2012
This is version 91 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program