EzCatDB: S00465
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DB codeS00465
RLCP classification2.15.32480.334 : Phosphorolysis
3.133.90010.334 : Transfer
CATH domainDomain 13.90.550.10 : Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain ACatalytic domain
E.C.2.7.7.24

CATH domainRelated DB codes (homologues)
3.90.550.10 : Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain AS00709,S00466,D00417,D00859,D00860,T00415

Enzyme Name
UniProtKBKEGG

P37744P61887Q9HU22Q9F7K6Q9F7G8
Protein nameGlucose-1-phosphate thymidylyltransferase 1Glucose-1-phosphate thymidylyltransferase 2Glucose-1-phosphate thymidylyltransferaseGlucose-1-phosphate thymidylyltransferaseGlucose-1-phosphate thymidylyltransferaseglucose-1-phosphate thymidylyltransferase
glucose 1-phosphate thymidylyltransferase
dTDP-glucose synthase
dTDP-glucose pyrophosphorylase
thymidine diphosphoglucose pyrophosphorylase
thymidine diphosphate glucose pyrophosphorylase
TDP-glucose pyrophosphorylase
SynonymsG1P-TT 1
EC 2.7.7.24
dTDP-glucose synthase 1
dTDP-glucose pyrophosphorylase 1
G1P-TT 2
EC 2.7.7.24
dTDP-glucose synthase 2
dTDP-glucose pyrophosphorylase 2
EC 2.7.7.24
EC 2.7.7.24
EC 2.7.7.24
RefSeqNP_416543.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_490281.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
NP_418236.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491650.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
NP_253850.1 (Protein)
NC_002516.2 (DNA/RNA sequence)


PfamPF00483 (NTP_transferase)
[Graphical view]
PF00483 (NTP_transferase)
[Graphical view]
PF00483 (NTP_transferase)
[Graphical view]
PF00483 (NTP_transferase)
[Graphical view]
PF00483 (NTP_transferase)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00520Nucleotide sugars metabolism
MAP00521Streptomycin biosynthesis
MAP00523Polyketide sugar unit biosynthesis

UniProtKB:Accession NumberP37744P61887Q9HU22Q9F7K6Q9F7G8
Entry nameRMLA1_ECOLIRMLA2_ECOLIQ9HU22_PSEAEQ9F7K6_9ENTRQ9F7G8_9ENTR
ActivitydTTP + alpha-D-glucose 1-phosphate = diphosphate + dTDP-glucose.dTTP + alpha-D-glucose 1-phosphate = diphosphate + dTDP-glucose.dTTP + alpha-D-glucose 1-phosphate = diphosphate + dTDP-glucose.dTTP + alpha-D-glucose 1-phosphate = diphosphate + dTDP-glucose.dTTP + alpha-D-glucose 1-phosphate = diphosphate + dTDP-glucose.
SubunitHomotetramer.Homotetramer, arranged as a dimer of dimers.


Subcellular location




CofactorBinds 1 magnesium ion per subunit (Probable).Binds 1 magnesium ion per subunit.



Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00305C00459C00103C00013C00842
CompoundMagnesiumdTTPalpha-D-Glucose 1-phosphatePyrophosphatedTDP-glucose
Typedivalent metal (Ca2+, Mg2+)amide group,nucleotidecarbohydrate,phosphate group/phosphate ionphosphate group/phosphate ionamide group,carbohydrate,nucleotide
ChEBI18420
18077
29042
29888
15700
PubChem888
64968
65533
21961011
1023
443210
             
1h5tAUnboundUnboundUnboundUnboundBound:DAU
1h5tBUnboundUnboundUnboundUnboundBound:DAU
1h5tCUnboundUnboundUnboundUnboundBound:DAU
1h5tDUnboundUnboundUnboundUnboundBound:DAU
1h5sAUnboundAnalogue:TMP 1293UnboundUnboundUnbound
1h5sBUnboundAnalogue:TMP 1293UnboundUnboundUnbound
1h5sCUnboundAnalogue:TMP 1293UnboundUnboundUnbound
1h5sDUnboundAnalogue:TMP 1293UnboundUnboundUnbound
1h5rAUnboundAnalogue:THM 1293Bound:G1PUnboundUnbound
1h5rBUnboundAnalogue:THM 1293Bound:G1PUnboundUnbound
1h5rCUnboundAnalogue:THM 1293Bound:G1PUnboundUnbound
1h5rDUnboundAnalogue:THM 1293Bound:G1PUnboundUnbound
1mc3ABound:_MGBound:TTPUnboundUnboundUnbound
1mc3BBound:_MGBound:TTPUnboundUnboundUnbound
1fxoAUnboundAnalogue:TMP 8500UnboundUnboundUnbound
1fxoBUnboundAnalogue:TMP 9500UnboundUnboundUnbound
1fxoCUnboundAnalogue:TMP 9501UnboundUnboundUnbound
1fxoDUnboundAnalogue:TMP 9502UnboundUnboundUnbound
1fxoEUnboundAnalogue:TMP 9503UnboundUnboundUnbound
1fxoFUnboundAnalogue:TMP 9504UnboundUnboundUnbound
1fxoGUnboundAnalogue:TMP 9505UnboundUnboundUnbound
1fxoHUnboundAnalogue:TMP 9506UnboundUnboundUnbound
1fzwAUnboundUnboundUnboundUnboundUnbound
1fzwBUnboundUnboundUnboundUnboundUnbound
1fzwCUnboundUnboundUnboundUnboundUnbound
1fzwDUnboundUnboundUnboundUnboundUnbound
1fzwEUnboundUnboundUnboundUnboundUnbound
1fzwFUnboundUnboundUnboundUnboundUnbound
1fzwGUnboundUnboundUnboundUnboundUnbound
1fzwHUnboundUnboundUnboundUnboundUnbound
1g0rAUnboundAnalogue:THM 2530Bound:G1PUnboundUnbound
1g0rBUnboundAnalogue:THM 2531Bound:G1PUnboundUnbound
1g0rCUnboundAnalogue:THM 2532Bound:G1PUnboundUnbound
1g0rDUnboundAnalogue:THM 2533Bound:G1PUnboundUnbound
1g0rEUnboundAnalogue:THM 2534Bound:G1PUnboundUnbound
1g0rFUnboundAnalogue:THM 2535UnboundUnboundUnbound
1g0rGUnboundAnalogue:THM 2536Bound:G1PUnboundUnbound
1g0rHUnboundAnalogue:THM 2537Bound:G1PUnboundUnbound
1g1lAUnboundUnboundUnboundUnboundBound:DAU 3500
1g1lBUnboundUnboundUnboundUnboundBound:DAU 3502
1g1lCUnboundUnboundUnboundUnboundBound:DAU 3504
1g1lDUnboundUnboundUnboundUnboundBound:DAU 3506
1g1lEUnboundUnboundUnboundUnboundBound:DAU 3508
1g1lFUnboundUnboundUnboundUnboundBound:DAU 3510
1g1lGUnboundUnboundUnboundUnboundBound:DAU 3514
1g1lHUnboundUnboundUnboundUnboundBound:DAU 3512
1g23AUnboundUnboundBound:G1PUnboundUnbound
1g23BUnboundUnboundBound:G1PUnboundUnbound
1g23CUnboundUnboundBound:G1PUnboundUnbound
1g23DUnboundUnboundBound:G1PUnboundUnbound
1g23EUnboundUnboundBound:G1PUnboundUnbound
1g23FUnboundUnboundBound:G1PUnboundUnbound
1g23GUnboundUnboundBound:G1PUnboundUnbound
1g23HUnboundUnboundBound:G1PUnboundUnbound
1g2vAUnboundBound:TTP 3500UnboundUnboundUnbound
1g2vBUnboundBound:TTP 3502UnboundUnboundUnbound
1g2vCUnboundBound:TTP 3504UnboundUnboundUnbound
1g2vDUnboundBound:TTP 3506UnboundUnboundUnbound
1g2vEUnboundBound:TTP 3508UnboundUnboundUnbound
1g2vFUnboundBound:TTP 3510UnboundUnboundUnbound
1g2vGUnboundBound:TTP 3512UnboundUnboundUnbound
1g2vHUnboundBound:TTP 3514UnboundUnboundUnbound
1g3lAUnboundUnboundUnboundUnboundAnalogue:TRH 500
1g3lBUnboundUnboundUnboundUnboundAnalogue:TRH 502
1g3lCUnboundUnboundUnboundUnboundAnalogue:TRH 504
1g3lDUnboundUnboundUnboundUnboundAnalogue:TRH 506
1iimAUnboundBound:TTP 501UnboundUnboundUnbound
1iimBUnboundBound:TTP 503UnboundUnboundUnbound
1iinAUnboundUnboundUnboundUnboundAnalogue:UPG
1iinBUnboundUnboundUnboundUnboundAnalogue:UPG
1iinCUnboundUnboundUnboundUnboundAnalogue:UPG
1iinDUnboundUnboundUnboundUnboundAnalogue:UPG
1mp3AUnboundBound:TTP 501UnboundUnboundUnbound
1mp3BUnboundBound:TTP 503UnboundUnboundUnbound
1mp4AUnboundUnboundUnboundUnboundAnalogue:UPG
1mp4BUnboundUnboundUnboundUnboundAnalogue:UPG
1mp5AUnboundUnboundUnboundUnboundAnalogue:UPG
1mp5BUnboundUnboundUnboundUnboundAnalogue:UPG
1mp5CUnboundUnboundUnboundUnboundAnalogue:UPG
1mp5DUnboundUnboundUnboundUnboundAnalogue:UPG

Active-site residues
resource
literature [2], [5]
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysiscomment
            
1h5tAARG 16;LYS 163;ARG 195
ASP 111;ASP 226(Magnesium binding)
SER 13;GLY 14;THR 15
 
1h5tBARG 16;LYS 163;ARG 195
ASP 111;ASP 226(Magnesium binding)
SER 13;GLY 14;THR 15
 
1h5tCARG 16;LYS 163;ARG 195
ASP 111;ASP 226(Magnesium binding)
SER 13;GLY 14;THR 15
 
1h5tDARG 16;LYS 163;ARG 195
ASP 111;ASP 226(Magnesium binding)
SER 13;GLY 14;THR 15
 
1h5sAARG 16;LYS 163;ARG 195
ASP 111;ASP 226(Magnesium binding)
SER 13;GLY 14;THR 15
 
1h5sBARG 16;LYS 163;ARG 195
ASP 111;ASP 226(Magnesium binding)
SER 13;GLY 14;THR 15
 
1h5sCARG 16;LYS 163;ARG 195
ASP 111;ASP 226(Magnesium binding)
SER 13;GLY 14;THR 15
 
1h5sDARG 16;LYS 163;ARG 195
ASP 111;ASP 226(Magnesium binding)
SER 13;GLY 14;THR 15
 
1h5rAARG 16;LYS 163;ARG 195
ASP 111;ASP 226(Magnesium binding)
SER 13;GLY 14;THR 15
 
1h5rBARG 16;LYS 163;ARG 195
ASP 111;ASP 226(Magnesium binding)
SER 13;GLY 14;THR 15
 
1h5rCARG 16;LYS 163;ARG 195
ASP 111;ASP 226(Magnesium binding)
SER 13;GLY 14;THR 15
 
1h5rDARG 16;LYS 163;ARG 195
ASP 111;ASP 226(Magnesium binding)
SER 13;GLY 14;THR 15
 
1mc3AARG 13;LYS 160;ARG 192
ASP 108;ASP 223(Magnesium binding)
SER 10;GLY 11;THR 12
 
1mc3BARG 13;LYS 160;ARG 192
ASP 108;ASP 223(Magnesium binding)
SER 10;GLY 11;THR 12
 
1fxoAARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1fxoBARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1fxoCARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1fxoDARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1fxoEARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1fxoFARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1fxoGARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1fxoHARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1fzwAARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1fzwBARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1fzwCARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1fzwDARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1fzwEARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1fzwFARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1fzwGARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1fzwHARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g0rAARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g0rBARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g0rCARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g0rDARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g0rEARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g0rFARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g0rGARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g0rHARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g1lAARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g1lBARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g1lCARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g1lDARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g1lEARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g1lFARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g1lGARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g1lHARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g23AARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
Modified by selenium S35, S44, S217
1g23BARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
Modified by selenium S35, S44, S217
1g23CARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
Modified by selenium S35, S44, S217
1g23DARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
Modified by selenium S35, S44, S217
1g23EARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
Modified by selenium S35, S44, S217
1g23FARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
Modified by selenium S35, S44, S217
1g23GARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
Modified by selenium S35, S44, S217
1g23HARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
Modified by selenium S35, S44, S217
1g2vAARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g2vBARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g2vCARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g2vDARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g2vEARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g2vFARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g2vGARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g2vHARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g3lAARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g3lBARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g3lCARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1g3lDARG 15;LYS 162;ARG 194
ASP 110;ASP 225(Magnesium binding)
SER 12;GLY 13;THR 14
 
1iimAARG 16;LYS 163;ARG 195
ASP 111;ASP 226(Magnesium binding)
SER 13;GLY 14;THR 15
 
1iimBARG 16;LYS 163;ARG 195
ASP 111;ASP 226(Magnesium binding)
SER 13;GLY 14;THR 15
 
1iinAARG 16;LYS 163;ARG 195
ASP 111;ASP 226(Magnesium binding)
SER 13;GLY 14;THR 15
 
1iinBARG 16;LYS 163;ARG 195
ASP 111;ASP 226(Magnesium binding)
SER 13;GLY 14;THR 15
 
1iinCARG 16;LYS 163;ARG 195
ASP 111;ASP 226(Magnesium binding)
SER 13;GLY 14;THR 15
 
1iinDARG 16;LYS 163;ARG 195
ASP 111;ASP 226(Magnesium binding)
SER 13;GLY 14;THR 15
 
1mp3AARG 16;LYS 163;ARG 195
ASP 111;ASP 226(Magnesium binding)
SER 13;GLY 14;THR 15
 
1mp3BARG 16;LYS 163;ARG 195
ASP 111;ASP 226(Magnesium binding)
SER 13;GLY 14;THR 15
 
1mp4AARG 16;LYS 163;ARG 195
ASP 111;ASP 226(Magnesium binding)
SER 13;GLY 14;THR 15
 
1mp4BARG 16;LYS 163;ARG 195
ASP 111;ASP 226(Magnesium binding)
SER 13;GLY 14;THR 15
 
1mp5AARG 16;LYS 163;ARG 195
ASP 111;ASP 226(Magnesium binding)
SER 13;GLY 14;THR 15
 
1mp5BARG 16;LYS 163;ARG 195
ASP 111;ASP 226(Magnesium binding)
SER 13;GLY 14;THR 15
 
1mp5CARG 16;LYS 163;ARG 195
ASP 111;ASP 226(Magnesium binding)
SER 13;GLY 14;THR 15
 
1mp5DARG 16;LYS 163;ARG 195
ASP 111;ASP 226(Magnesium binding)
SER 13;GLY 14;THR 15
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]Fig.1A, p.6657-66581
[3]p.838-840
[4]p.548-549
[5]p.44217-44219

references
[1]
PubMed ID11053865
JournalActa Crystallogr D Biol Crystallogr
Year2000
Volume56
Pages1501-4
AuthorsBlankenfeldt W, Giraud MF, Leonard G, Rahim R, Creuzenet C, Lam JS, Naismith JH
TitleThe 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.
[2]
CommentsX-ray crystallography
PubMed ID11118200
JournalEMBO J
Year2000
Volume19
Pages6652-63
AuthorsBlankenfeldt W, Asuncion M, Lam JS, Naismith JH
TitleThe structural basis of the catalytic mechanism and regulation of glucose-1-phosphate thymidylyltransferase (RmlA).
Related PDB1fxo,1fzw,1g0r,1g1l,1g23,1g2v,1g3l
[3]
PubMed ID11697907
JournalJ Mol Biol
Year2001
Volume313
Pages831-43
AuthorsZuccotti S, Zanardi D, Rosano C, Sturla L, Tonetti M, Bolognesi M
TitleKinetic and crystallographic analyses support a sequential-ordered bi bi catalytic mechanism for Escherichia coli glucose-1-phosphate thymidylyltransferase.
Related PDB1h5r,1h5s,1h5t
[4]
PubMed ID11373625
JournalNat Struct Biol
Year2001
Volume8
Pages545-51
AuthorsBarton WA, Lesniak J, Biggins JB, Jeffrey PD, Jiang J, Rajashankar KR, Thorson JS, Nikolov DB
TitleStructure, mechanism and engineering of a nucleotidylyltransferase as a first step toward glycorandomization.
Related PDB1iim,1iin
[5]
PubMed ID12171937
JournalJ Biol Chem
Year2002
Volume277
Pages44214-9
AuthorsSivaraman J, Sauve V, Matte A, Cygler M
TitleCrystal structure of Escherichia coli glucose-1-phosphate thymidylyltransferase (RffH) complexed with dTTP and Mg2+.
Related PDB1mc3
[6]
PubMed ID12374866
JournalProc Natl Acad Sci U S A
Year2002
Volume99
Pages13397-402
AuthorsBarton WA, Biggins JB, Jiang J, Thorson JS, Nikolov DB
TitleExpanding pyrimidine diphosphosugar libraries via structure-based nucleotidylyltransferase engineering.
Related PDB1mp3,1mp4,1mp5

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.

createdupdated
2003-07-142011-06-06


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
© Biotechnology Research Institute for Drug Discovery, AIST, 2015-2016 All Rights Reserved.
© Computational Biology Research Center, AIST, 2004-2016 All Rights Reserved.