DB code: S00465

RLCP classification 2.15.32480.334 : Phosphorolysis
3.133.90010.334 : Transfer
CATH domain 3.90.550.10 : Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A Catalytic domain
E.C. 2.7.7.24
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.90.550.10 : Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A S00709 S00466 D00417 D00859 D00860 T00415

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P37744 Glucose-1-phosphate thymidylyltransferase 1
G1P-TT 1
EC 2.7.7.24
dTDP-glucose synthase 1
dTDP-glucose pyrophosphorylase 1
NP_416543.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_490281.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF00483 (NTP_transferase)
[Graphical View]
P61887 Glucose-1-phosphate thymidylyltransferase 2
G1P-TT 2
EC 2.7.7.24
dTDP-glucose synthase 2
dTDP-glucose pyrophosphorylase 2
NP_418236.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491650.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF00483 (NTP_transferase)
[Graphical View]
Q9HU22 Glucose-1-phosphate thymidylyltransferase
EC 2.7.7.24
NP_253850.1 (Protein)
NC_002516.2 (DNA/RNA sequence)
PF00483 (NTP_transferase)
[Graphical View]
Q9F7K6 Glucose-1-phosphate thymidylyltransferase
EC 2.7.7.24
PF00483 (NTP_transferase)
[Graphical View]
Q9F7G8 Glucose-1-phosphate thymidylyltransferase
EC 2.7.7.24
PF00483 (NTP_transferase)
[Graphical View]

KEGG enzyme name
glucose-1-phosphate thymidylyltransferase
glucose 1-phosphate thymidylyltransferase
dTDP-glucose synthase
dTDP-glucose pyrophosphorylase
thymidine diphosphoglucose pyrophosphorylase
thymidine diphosphate glucose pyrophosphorylase
TDP-glucose pyrophosphorylase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P37744 RMLA1_ECOLI dTTP + alpha-D-glucose 1-phosphate = diphosphate + dTDP-glucose. Homotetramer. Binds 1 magnesium ion per subunit (Probable).
P61887 RMLA2_ECOLI dTTP + alpha-D-glucose 1-phosphate = diphosphate + dTDP-glucose. Homotetramer, arranged as a dimer of dimers. Binds 1 magnesium ion per subunit.
Q9HU22 Q9HU22_PSEAE dTTP + alpha-D-glucose 1-phosphate = diphosphate + dTDP-glucose.
Q9F7K6 Q9F7K6_9ENTR dTTP + alpha-D-glucose 1-phosphate = diphosphate + dTDP-glucose.
Q9F7G8 Q9F7G8_9ENTR dTTP + alpha-D-glucose 1-phosphate = diphosphate + dTDP-glucose.

KEGG Pathways
Map code Pathways E.C.
MAP00520 Nucleotide sugars metabolism
MAP00521 Streptomycin biosynthesis
MAP00523 Polyketide sugar unit biosynthesis

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00459 C00103 C00013 C00842
E.C.
Compound Magnesium dTTP alpha-D-Glucose 1-phosphate Pyrophosphate dTDP-glucose
Type divalent metal (Ca2+, Mg2+) amide group,nucleotide carbohydrate,phosphate group/phosphate ion phosphate group/phosphate ion amide group,carbohydrate,nucleotide
ChEBI 18420
 18420
 		18077
 18077
 		29042
 29042
 		29888
 29888
 		15700
 15700
PubChem 888
 888
 		64968
 64968
 		65533
 65533
 		1023
 21961011
 1023
 21961011
 		443210
 443210
1h5tA Unbound Unbound Unbound Unbound Bound:DAU
1h5tB Unbound Unbound Unbound Unbound Bound:DAU
1h5tC Unbound Unbound Unbound Unbound Bound:DAU
1h5tD Unbound Unbound Unbound Unbound Bound:DAU
1h5sA Unbound Analogue:TMP_1293 Unbound Unbound Unbound
1h5sB Unbound Analogue:TMP_1293 Unbound Unbound Unbound
1h5sC Unbound Analogue:TMP_1293 Unbound Unbound Unbound
1h5sD Unbound Analogue:TMP_1293 Unbound Unbound Unbound
1h5rA Unbound Analogue:THM_1293 Bound:G1P Unbound Unbound
1h5rB Unbound Analogue:THM_1293 Bound:G1P Unbound Unbound
1h5rC Unbound Analogue:THM_1293 Bound:G1P Unbound Unbound
1h5rD Unbound Analogue:THM_1293 Bound:G1P Unbound Unbound
1mc3A Bound:_MG Bound:TTP Unbound Unbound Unbound
1mc3B Bound:_MG Bound:TTP Unbound Unbound Unbound
1fxoA Unbound Analogue:TMP_8500 Unbound Unbound Unbound
1fxoB Unbound Analogue:TMP_9500 Unbound Unbound Unbound
1fxoC Unbound Analogue:TMP_9501 Unbound Unbound Unbound
1fxoD Unbound Analogue:TMP_9502 Unbound Unbound Unbound
1fxoE Unbound Analogue:TMP_9503 Unbound Unbound Unbound
1fxoF Unbound Analogue:TMP_9504 Unbound Unbound Unbound
1fxoG Unbound Analogue:TMP_9505 Unbound Unbound Unbound
1fxoH Unbound Analogue:TMP_9506 Unbound Unbound Unbound
1fzwA Unbound Unbound Unbound Unbound Unbound
1fzwB Unbound Unbound Unbound Unbound Unbound
1fzwC Unbound Unbound Unbound Unbound Unbound
1fzwD Unbound Unbound Unbound Unbound Unbound
1fzwE Unbound Unbound Unbound Unbound Unbound
1fzwF Unbound Unbound Unbound Unbound Unbound
1fzwG Unbound Unbound Unbound Unbound Unbound
1fzwH Unbound Unbound Unbound Unbound Unbound
1g0rA Unbound Analogue:THM_2530 Bound:G1P Unbound Unbound
1g0rB Unbound Analogue:THM_2531 Bound:G1P Unbound Unbound
1g0rC Unbound Analogue:THM_2532 Bound:G1P Unbound Unbound
1g0rD Unbound Analogue:THM_2533 Bound:G1P Unbound Unbound
1g0rE Unbound Analogue:THM_2534 Bound:G1P Unbound Unbound
1g0rF Unbound Analogue:THM_2535 Unbound Unbound Unbound
1g0rG Unbound Analogue:THM_2536 Bound:G1P Unbound Unbound
1g0rH Unbound Analogue:THM_2537 Bound:G1P Unbound Unbound
1g1lA Unbound Unbound Unbound Unbound Bound:DAU_3500
1g1lB Unbound Unbound Unbound Unbound Bound:DAU_3502
1g1lC Unbound Unbound Unbound Unbound Bound:DAU_3504
1g1lD Unbound Unbound Unbound Unbound Bound:DAU_3506
1g1lE Unbound Unbound Unbound Unbound Bound:DAU_3508
1g1lF Unbound Unbound Unbound Unbound Bound:DAU_3510
1g1lG Unbound Unbound Unbound Unbound Bound:DAU_3514
1g1lH Unbound Unbound Unbound Unbound Bound:DAU_3512
1g23A Unbound Unbound Bound:G1P Unbound Unbound
1g23B Unbound Unbound Bound:G1P Unbound Unbound
1g23C Unbound Unbound Bound:G1P Unbound Unbound
1g23D Unbound Unbound Bound:G1P Unbound Unbound
1g23E Unbound Unbound Bound:G1P Unbound Unbound
1g23F Unbound Unbound Bound:G1P Unbound Unbound
1g23G Unbound Unbound Bound:G1P Unbound Unbound
1g23H Unbound Unbound Bound:G1P Unbound Unbound
1g2vA Unbound Bound:TTP_3500 Unbound Unbound Unbound
1g2vB Unbound Bound:TTP_3502 Unbound Unbound Unbound
1g2vC Unbound Bound:TTP_3504 Unbound Unbound Unbound
1g2vD Unbound Bound:TTP_3506 Unbound Unbound Unbound
1g2vE Unbound Bound:TTP_3508 Unbound Unbound Unbound
1g2vF Unbound Bound:TTP_3510 Unbound Unbound Unbound
1g2vG Unbound Bound:TTP_3512 Unbound Unbound Unbound
1g2vH Unbound Bound:TTP_3514 Unbound Unbound Unbound
1g3lA Unbound Unbound Unbound Unbound Analogue:TRH_500
1g3lB Unbound Unbound Unbound Unbound Analogue:TRH_502
1g3lC Unbound Unbound Unbound Unbound Analogue:TRH_504
1g3lD Unbound Unbound Unbound Unbound Analogue:TRH_506
1iimA Unbound Bound:TTP_501 Unbound Unbound Unbound
1iimB Unbound Bound:TTP_503 Unbound Unbound Unbound
1iinA Unbound Unbound Unbound Unbound Analogue:UPG
1iinB Unbound Unbound Unbound Unbound Analogue:UPG
1iinC Unbound Unbound Unbound Unbound Analogue:UPG
1iinD Unbound Unbound Unbound Unbound Analogue:UPG
1mp3A Unbound Bound:TTP_501 Unbound Unbound Unbound
1mp3B Unbound Bound:TTP_503 Unbound Unbound Unbound
1mp4A Unbound Unbound Unbound Unbound Analogue:UPG
1mp4B Unbound Unbound Unbound Unbound Analogue:UPG
1mp5A Unbound Unbound Unbound Unbound Analogue:UPG
1mp5B Unbound Unbound Unbound Unbound Analogue:UPG
1mp5C Unbound Unbound Unbound Unbound Analogue:UPG
1mp5D Unbound Unbound Unbound Unbound Analogue:UPG

Reference for Active-site residues
resource references E.C.
literature [2], [5]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1h5tA ARG 16;LYS 163;ARG 195 ASP 111;ASP 226(Magnesium binding) SER 13;GLY 14;THR 15
1h5tB ARG 16;LYS 163;ARG 195 ASP 111;ASP 226(Magnesium binding) SER 13;GLY 14;THR 15
1h5tC ARG 16;LYS 163;ARG 195 ASP 111;ASP 226(Magnesium binding) SER 13;GLY 14;THR 15
1h5tD ARG 16;LYS 163;ARG 195 ASP 111;ASP 226(Magnesium binding) SER 13;GLY 14;THR 15
1h5sA ARG 16;LYS 163;ARG 195 ASP 111;ASP 226(Magnesium binding) SER 13;GLY 14;THR 15
1h5sB ARG 16;LYS 163;ARG 195 ASP 111;ASP 226(Magnesium binding) SER 13;GLY 14;THR 15
1h5sC ARG 16;LYS 163;ARG 195 ASP 111;ASP 226(Magnesium binding) SER 13;GLY 14;THR 15
1h5sD ARG 16;LYS 163;ARG 195 ASP 111;ASP 226(Magnesium binding) SER 13;GLY 14;THR 15
1h5rA ARG 16;LYS 163;ARG 195 ASP 111;ASP 226(Magnesium binding) SER 13;GLY 14;THR 15
1h5rB ARG 16;LYS 163;ARG 195 ASP 111;ASP 226(Magnesium binding) SER 13;GLY 14;THR 15
1h5rC ARG 16;LYS 163;ARG 195 ASP 111;ASP 226(Magnesium binding) SER 13;GLY 14;THR 15
1h5rD ARG 16;LYS 163;ARG 195 ASP 111;ASP 226(Magnesium binding) SER 13;GLY 14;THR 15
1mc3A ARG 13;LYS 160;ARG 192 ASP 108;ASP 223(Magnesium binding) SER 10;GLY 11;THR 12
1mc3B ARG 13;LYS 160;ARG 192 ASP 108;ASP 223(Magnesium binding) SER 10;GLY 11;THR 12
1fxoA ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1fxoB ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1fxoC ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1fxoD ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1fxoE ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1fxoF ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1fxoG ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1fxoH ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1fzwA ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1fzwB ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1fzwC ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1fzwD ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1fzwE ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1fzwF ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1fzwG ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1fzwH ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g0rA ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g0rB ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g0rC ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g0rD ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g0rE ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g0rF ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g0rG ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g0rH ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g1lA ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g1lB ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g1lC ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g1lD ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g1lE ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g1lF ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g1lG ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g1lH ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g23A ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14 Modified by selenium S35, S44, S217
1g23B ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14 Modified by selenium S35, S44, S217
1g23C ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14 Modified by selenium S35, S44, S217
1g23D ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14 Modified by selenium S35, S44, S217
1g23E ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14 Modified by selenium S35, S44, S217
1g23F ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14 Modified by selenium S35, S44, S217
1g23G ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14 Modified by selenium S35, S44, S217
1g23H ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14 Modified by selenium S35, S44, S217
1g2vA ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g2vB ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g2vC ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g2vD ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g2vE ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g2vF ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g2vG ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g2vH ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g3lA ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g3lB ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g3lC ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1g3lD ARG 15;LYS 162;ARG 194 ASP 110;ASP 225(Magnesium binding) SER 12;GLY 13;THR 14
1iimA ARG 16;LYS 163;ARG 195 ASP 111;ASP 226(Magnesium binding) SER 13;GLY 14;THR 15
1iimB ARG 16;LYS 163;ARG 195 ASP 111;ASP 226(Magnesium binding) SER 13;GLY 14;THR 15
1iinA ARG 16;LYS 163;ARG 195 ASP 111;ASP 226(Magnesium binding) SER 13;GLY 14;THR 15
1iinB ARG 16;LYS 163;ARG 195 ASP 111;ASP 226(Magnesium binding) SER 13;GLY 14;THR 15
1iinC ARG 16;LYS 163;ARG 195 ASP 111;ASP 226(Magnesium binding) SER 13;GLY 14;THR 15
1iinD ARG 16;LYS 163;ARG 195 ASP 111;ASP 226(Magnesium binding) SER 13;GLY 14;THR 15
1mp3A ARG 16;LYS 163;ARG 195 ASP 111;ASP 226(Magnesium binding) SER 13;GLY 14;THR 15
1mp3B ARG 16;LYS 163;ARG 195 ASP 111;ASP 226(Magnesium binding) SER 13;GLY 14;THR 15
1mp4A ARG 16;LYS 163;ARG 195 ASP 111;ASP 226(Magnesium binding) SER 13;GLY 14;THR 15
1mp4B ARG 16;LYS 163;ARG 195 ASP 111;ASP 226(Magnesium binding) SER 13;GLY 14;THR 15
1mp5A ARG 16;LYS 163;ARG 195 ASP 111;ASP 226(Magnesium binding) SER 13;GLY 14;THR 15
1mp5B ARG 16;LYS 163;ARG 195 ASP 111;ASP 226(Magnesium binding) SER 13;GLY 14;THR 15
1mp5C ARG 16;LYS 163;ARG 195 ASP 111;ASP 226(Magnesium binding) SER 13;GLY 14;THR 15
1mp5D ARG 16;LYS 163;ARG 195 ASP 111;ASP 226(Magnesium binding) SER 13;GLY 14;THR 15

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[2]
Fig.1A, p.6657-6658 1
[3]
p.838-840
[4]
p.548-549
[5]
p.44217-44219

References
[1]
Resource
Comments
Medline ID
PubMed ID 11053865
Journal Acta Crystallogr D Biol Crystallogr
Year 2000
Volume 56
Pages 1501-4
Authors Blankenfeldt W, Giraud MF, Leonard G, Rahim R, Creuzenet C, Lam JS, Naismith JH
Title The purification, crystallization and preliminary structural characterization of glucose-1-phosphate thymidylyltransferase (RmlA), the first enzyme of the dTDP-L-rhamnose synthesis pathway from Pseudomonas aeruginosa.
Related PDB
Related UniProtKB
[2]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 11118200
Journal EMBO J
Year 2000
Volume 19
Pages 6652-63
Authors Blankenfeldt W, Asuncion M, Lam JS, Naismith JH
Title The structural basis of the catalytic mechanism and regulation of glucose-1-phosphate thymidylyltransferase (RmlA).
Related PDB 1fxo 1fzw 1g0r 1g1l 1g23 1g2v 1g3l
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 11697907
Journal J Mol Biol
Year 2001
Volume 313
Pages 831-43
Authors Zuccotti S, Zanardi D, Rosano C, Sturla L, Tonetti M, Bolognesi M
Title Kinetic and crystallographic analyses support a sequential-ordered bi bi catalytic mechanism for Escherichia coli glucose-1-phosphate thymidylyltransferase.
Related PDB 1h5r 1h5s 1h5t
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 11373625
Journal Nat Struct Biol
Year 2001
Volume 8
Pages 545-51
Authors Barton WA, Lesniak J, Biggins JB, Jeffrey PD, Jiang J, Rajashankar KR, Thorson JS, Nikolov DB
Title Structure, mechanism and engineering of a nucleotidylyltransferase as a first step toward glycorandomization.
Related PDB 1iim 1iin
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 12171937
Journal J Biol Chem
Year 2002
Volume 277
Pages 44214-9
Authors Sivaraman J, Sauve V, Matte A, Cygler M
Title Crystal structure of Escherichia coli glucose-1-phosphate thymidylyltransferase (RffH) complexed with dTTP and Mg2+.
Related PDB 1mc3
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 12374866
Journal Proc Natl Acad Sci U S A
Year 2002
Volume 99
Pages 13397-402
Authors Barton WA, Biggins JB, Jiang J, Thorson JS, Nikolov DB
Title Expanding pyrimidine diphosphosugar libraries via structure-based nucleotidylyltransferase engineering.
Related PDB 1mp3 1mp4 1mp5
Related UniProtKB

Comments
According to the literature [2], [3], [4] & [5], in the crystal structures except for 1mc3 (Swiss-prot;P61887), magnesium ion has not been found. Moreover, the literature [2] mentioned that the sidechain of Asp110, which is supposed to be bound to magnesium ion, is close to the transferred group, alpha-phosphate group of products, dTDP-Glc. It is very unlikely due to the repulsion between the negatively charged atoms, according to the paper [5].
According to the literature [5], the cofactor, magnesium ion, seems to be interacting with both transferred and acceptor groups, the alpha-phosphate of dTTP and the phosphate group of the G1P substrate. This cofactor probably bridges the two groups, and neutralizes the negative charge on the groups. On the other hand, mainchain amide groups from Ser10-Gly11-Thr12 and sidechain of Arg15 (of 1mc3) interact mainly with the leaving group, beta- and gamma-phosphate groups of dTTP, or the pyrophosphate product, whilst Lys160 and Arg192 interact with the acceptor group, the phosphate group of Glc-1-phosphate. These residues act as stabilizer during catalysis.
Taken together, the catalytic reaction proceeds by a single displacement mechanism, as follows:
(1) The acceptor group, the phosphoryl oxygen of Glc-1-phosphate, whose negative charge is neutralized by the cofactor magnesium ion and Lys160/Arg192, makes a nucleophilic attack on the transferred group, the phosphorus atom of alpha-phosphate of dTTP. This reaction proceeds through an SN2-type mechanism, where the attacking oxygen atom is in-line with the P-O bond between the transferred phosphate and leaving oxygen atom.
(2) The pentacovalent transtion state must be stabilized by the cofactor magnesium ion and stabilizer residues, Lys162/Arg192.
(3) Finally, the leaving pyrophosphate is cleaved from the dTTP, to form dTDP-Glc.
Moreover, the reverse reaction is phosphorolysis of phosphoric ester bond between the two phosphate groups.

Created Updated
2003-07-14 2011-06-06