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 16108	17158 17158	26078 26078
PubChem	668 668	880 880	1004 22486802 1004 22486802

1b93A	Unbound	Unbound	Unbound	Unbound
1b93B	Unbound	Unbound	Bound:PO4	Unbound
1b93C	Unbound	Unbound	Unbound	Unbound
1eghA	Unbound	Unbound	Unbound	1st-Transition-state-analogue:PGA
1eghB	Unbound	Unbound	Unbound	1st-Transition-state-analogue:PGA
1eghC	Unbound	Unbound	Unbound	1st-Transition-state-analogue:PGA
1eghD	Unbound	Unbound	Unbound	1st-Transition-state-analogue:PGA
1eghE	Unbound	Unbound	Unbound	1st-Transition-state-analogue:PGA
1eghF	Unbound	Unbound	Unbound	1st-Transition-state-analogue:PGA
1ik4A	Unbound	Unbound	Unbound	2nd-Transition-state-analogue:PGH
1ik4B	Unbound	Unbound	Unbound	2nd-Transition-state-analogue:PGH
1ik4C	Unbound	Unbound	Unbound	2nd-Transition-state-analogue:PGH
1ik4D	Unbound	Unbound	Unbound	2nd-Transition-state-analogue:PGH
1ik4E	Unbound	Unbound	Unbound	2nd-Transition-state-analogue:PGH
1ik4F	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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.

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