DB code: S00370

RLCP classification 5.1304.666000.68 : Elimination
CATH domain 3.40.50.1380 : Rossmann fold Catalytic domain
E.C. 4.2.3.3
CSA 1b93
M-CSA 1b93
MACiE M0085

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P0A731 Methylglyoxal synthase
MGS
EC 4.2.3.3
NP_415483.2 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_489235.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF02142 (MGS)
[Graphical View]

KEGG enzyme name
methylglyoxal synthase
methylglyoxal synthetase
glycerone-phosphate phospho-lyase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P0A731 MGSA_ECOLI Glycerone phosphate = methylglyoxal + phosphate. Homohexamer. Cytoplasm.

KEGG Pathways
Map code Pathways E.C.
MAP00620 Pyruvate metabolism

Compound table
Substrates Products Intermediates
KEGG-id C00111 C00546 C00009
E.C.
Compound Glycerone phosphate Methylglyoxal Orthophosphate literature [3] &
Type carbohydrate,phosphate group/phosphate ion carbohydrate phosphate group/phosphate ion [4]
ChEBI 16108
17158
26078
PubChem 668
880
1004
22486802
1b93A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1b93B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:PO4 Unbound
1b93C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1eghA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound 1st-Transition-state-analogue:PGA
1eghB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound 1st-Transition-state-analogue:PGA
1eghC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound 1st-Transition-state-analogue:PGA
1eghD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound 1st-Transition-state-analogue:PGA
1eghE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound 1st-Transition-state-analogue:PGA
1eghF Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound 1st-Transition-state-analogue:PGA
1ik4A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound 2nd-Transition-state-analogue:PGH
1ik4B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound 2nd-Transition-state-analogue:PGH
1ik4C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound 2nd-Transition-state-analogue:PGH
1ik4D Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound 2nd-Transition-state-analogue:PGH
1ik4E Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound 2nd-Transition-state-analogue:PGH
1ik4F Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound 2nd-Transition-state-analogue:PGH

Reference for Active-site residues
resource references E.C.
Swiss-prot;P0A731 & literature [3], [4]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1b93A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 23;THR 45;THR 47;THR 48;SER 65; (stabilize eliminated phosphate);HIS 19;ASP 71;HIS 98;ASP 101 THR 47;THR 48;GLY 66 inivisible 149-152
1b93B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 23;THR 45;THR 47;THR 48;SER 65;ARG 150(stabilize eliminated phosphate);HIS 19;ASP 71;HIS 98;ASP 101 THR 47;THR 48;GLY 66 R150 contributes to other chain
1b93C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 23;THR 45;THR 47;THR 48;SER 65; (stabilize eliminated phosphate);HIS 19;ASP 71;HIS 98;ASP 101 THR 47;THR 48;GLY 66 inivisible 149-152
1eghA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 23;THR 45;THR 47;THR 48;SER 65;ARG 150(stabilize eliminated phosphate);HIS 19;ASP 71;HIS 98;ASP 101 THR 47;THR 48;GLY 66 R150 contributes to other chain
1eghB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 23;THR 45;THR 47;THR 48;SER 65;ARG 150(stabilize eliminated phosphate);HIS 19;ASP 71;HIS 98;ASP 101 THR 47;THR 48;GLY 66 R150 contributes to other chain
1eghC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 23;THR 45;THR 47;THR 48;SER 65;ARG 150(stabilize eliminated phosphate);HIS 19;ASP 71;HIS 98;ASP 101 THR 47;THR 48;GLY 66 R150 contributes to other chain
1eghD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 23;THR 45;THR 47;THR 48;SER 65;ARG 150(stabilize eliminated phosphate);HIS 19;ASP 71;HIS 98;ASP 101 THR 47;THR 48;GLY 66 R150 contributes to other chain
1eghE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 23;THR 45;THR 47;THR 48;SER 65;ARG 150(stabilize eliminated phosphate);HIS 19;ASP 71;HIS 98;ASP 101 THR 47;THR 48;GLY 66 R150 contributes to other chain
1eghF Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 23;THR 45;THR 47;THR 48;SER 65;ARG 150(stabilize eliminated phosphate);HIS 19;ASP 71;HIS 98;ASP 101 THR 47;THR 48;GLY 66 R150 contributes to other chain
1ik4A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 23;THR 45;THR 47;THR 48;SER 65;ARG 150(stabilize eliminated phosphate);HIS 19;ASP 71;HIS 98;ASP 101 THR 47;THR 48;GLY 66 R150 contributes to other chain
1ik4B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 23;THR 45;THR 47;THR 48;SER 65;ARG 150(stabilize eliminated phosphate);HIS 19;ASP 71;HIS 98;ASP 101 THR 47;THR 48;GLY 66 R150 contributes to other chain
1ik4C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 23;THR 45;THR 47;THR 48;SER 65;ARG 150(stabilize eliminated phosphate);HIS 19;ASP 71;HIS 98;ASP 101 THR 47;THR 48;GLY 66 R150 contributes to other chain
1ik4D Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 23;THR 45;THR 47;THR 48;SER 65;ARG 150(stabilize eliminated phosphate);HIS 19;ASP 71;HIS 98;ASP 101 THR 47;THR 48;GLY 66 R150 contributes to other chain
1ik4E Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 23;THR 45;THR 47;THR 48;SER 65;ARG 150(stabilize eliminated phosphate);HIS 19;ASP 71;HIS 98;ASP 101 THR 47;THR 48;GLY 66 R150 contributes to other chain
1ik4F Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 23;THR 45;THR 47;THR 48;SER 65;ARG 150(stabilize eliminated phosphate);HIS 19;ASP 71;HIS 98;ASP 101 THR 47;THR 48;GLY 66 R150 contributes to other chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
Fig.7b, p.10084 2
[2]
Fig.1 3
[3]
eq 1, Fig.5a, Fig.7, p.2954-2958 2
[4]
Fig.12, Fig.13, p.6815-6817 5
[6]
Scheme 1

References
[1]
Resource
Comments MUTAGENESIS OF ASPARTIC ACID RESIDUES.
Medline ID 98332530
PubMed ID 9665712
Journal Biochemistry
Year 1998
Volume 37
Pages 10074-86
Authors Saadat D, Harrison DH
Title Identification of catalytic bases in the active site of Escherichia coli methylglyoxal synthase: cloning, expression, and functional characterization of conserved aspartic acid residues.
Related PDB
Related UniProtKB P0A731
[2]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
Medline ID 99197296
PubMed ID 10368300
Journal Structure Fold Des
Year 1999
Volume 7
Pages 309-17
Authors Saadat D, Harrison DH
Title The crystal structure of methylglyoxal synthase from Escherichia coli.
Related PDB 1b93
Related UniProtKB P0A731
[3]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID 20181667
PubMed ID 10715115
Journal Biochemistry
Year 2000
Volume 39
Pages 2950-60
Authors Saadat D, Harrison DH
Title Mirroring perfection: the structure of methylglyoxal synthase complexed with the competitive inhibitor 2-phosphoglycolate.
Related PDB 1egh
Related UniProtKB P0A731
[4]
Resource
Comments
Medline ID
PubMed ID 11389594
Journal Biochemistry
Year 2001
Volume 40
Pages 6805-18
Authors Marks GT, Harris TK, Massiah MA, Mildvan AS, Harrison DH
Title Mechanistic implications of methylglyoxal synthase complexed with phosphoglycolohydroxamic acid as observed by X-ray crystallography and NMR spectroscopy.
Related PDB 1ik4
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 12405831
Journal J Am Chem Soc
Year 2002
Volume 124
Pages 13047-52
Authors Rose IA, Nowick JS
Title Methylglyoxal synthetase, enol-pyruvaldehyde, glutathione and the glyoxalase system.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 12475328
Journal J Am Chem Soc
Year 2002
Volume 124
Pages 14871-8
Authors Zhang X, Harrison DH, Cui Q
Title Functional specificities of methylglyoxal synthase and triosephosphate isomerase: a combined QM/MM analysis.
Related PDB
Related UniProtKB

Comments
This enzyme was transferred from E.C. 4.2.99.11 to E.C. 4.2.3.3.
This enzyme catalyzes two successive reactions:
(A) Isomerization (change in the position of double-bond).
(B) Elimination of phosphate group (This is not beta-elimination, as the elimination site and deprotonation site are not adjacent to each other, 3-bonds away via a double-bond).
According to the literature [3] & [4], two possible catalytic mechanisms have been proposed. One is similar to that of triosephosphate isomerase (TIM), suggesting that His98 might act both as a general acid and as a general base. On the other hand, another mechanism, in which His98 function as a stabilizer of transition-states, is more likely, as it is supported by the X-ray crystallography and NMR studies.
The latter mechanism proceeds as follows (see [4]):
(A) Isomerization (change in the position of double-bond).
(A1) At the initial stage, the pKa of Asp71 can be increased by the presence of the negative charge of Asp101, whilst the pKa of the C3 proton can be decreased by polarization of the 2-carbonyl group by His98. Moreover, His19 stabilizes the hydroxyl group (3-OH) of the substrate.
(A2) Asp71 acts as the first base, by abstracting the pro-S proton from the C3 carbon, resulting in the enediolic intermediate.
(A3) His98 and a bound water molecule (A) stabilize the negative charge formed on the O2 of the enodilate. Instead of a catalytic acid, the water donates the proton to the O2 atom, forming the hydroxyl group (2-OH).
(B) Elimination of phosphate group.
(B1) Asp101 modulates the protonation state of Asp71, by deprotonating the sidechain of Asp71 through a water molecule (B), as a proton scavenger. Here, Asp71 has to rotate its own sidechain to interact with the water.
(B2) The negetively charged carboxylate of Asp71 approaches the 3-OH on the enodiolic plane, whilst the elminated group, phosphate, is tilted out of the plane.
(B3) Asp71 acts again as a general base to abstract a proton from the 3-OH, whilst the elimination of the phosphate group is facilitated by the hydrogen bonds from the sidechains of Lys23, Thr45, Thr47, Thr48, Ser65 at the active site and Arg150 from the adjacent chain, and from the mainchain amide of Thr47, Thr48 and Gly66)
(B4) Finally, the enol form of methylglyoxal is released into solution, where it dissociates and isomerizes to its keton form.

Created Updated
2004-06-28 2009-02-26