EzCatDB: S00370

DB codeS00370
RLCP classification5.1304.666000.68
CATH domainDomain 13.40.50.1380Catalytic domain
E.C.4.2.3.3
CSA1b93
MACiEM0085


Enzyme Name
Swiss-protKEGG

P0A731
Protein nameMethylglyoxal synthasemethylglyoxal synthase
methylglyoxal synthetase
glycerone-phosphate phospho-lyase
SynonymsMGS
EC 4.2.3.3

KEGG pathways
MAP codePathways
MAP00620Pyruvate metabolism

Swiss-prot:Accession NumberP0A731
Entry nameMGSA_ECOLI
ActivityGlycerone phosphate = methylglyoxal + phosphate.
SubunitHomohexamer.
Subcellular locationCytoplasm.
Cofactor


SubstratesProductsintermediates
KEGG-idC00111C00546C00009
CompoundGlycerone phosphateMethylglyoxalOrthophosphateliterature [3] &
Typecarbohydrate,phosphate group/phosphate ioncarbohydratephosphate group/phosphate ionreffernce[4]
1b93AUnboundUnboundUnboundUnbound
1b93BUnboundUnboundBound:PO4Unbound
1b93CUnboundUnboundUnboundUnbound
1eghAUnboundUnboundUnbound1st-Transition-state-analogue:PGA
1eghBUnboundUnboundUnbound1st-Transition-state-analogue:PGA
1eghCUnboundUnboundUnbound1st-Transition-state-analogue:PGA
1eghDUnboundUnboundUnbound1st-Transition-state-analogue:PGA
1eghEUnboundUnboundUnbound1st-Transition-state-analogue:PGA
1eghFUnboundUnboundUnbound1st-Transition-state-analogue:PGA
1ik4AUnboundUnboundUnbound2nd-Transition-state-analogue:PGH
1ik4BUnboundUnboundUnbound2nd-Transition-state-analogue:PGH
1ik4CUnboundUnboundUnbound2nd-Transition-state-analogue:PGH
1ik4DUnboundUnboundUnbound2nd-Transition-state-analogue:PGH
1ik4EUnboundUnboundUnbound2nd-Transition-state-analogue:PGH
1ik4FUnboundUnboundUnbound2nd-Transition-state-analogue:PGH

Active-site residues
resource
Swiss-prot;P0A731 & literature [3], [4]
pdbCatalytic residuesMain-chain involved in catalysiscomment
1b93ALYS 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
1b93BLYS 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
1b93CLYS 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
1eghALYS 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
1eghBLYS 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
1eghCLYS 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
1eghDLYS 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
1eghELYS 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
1eghFLYS 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
1ik4ALYS 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
1ik4BLYS 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
1ik4CLYS 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
1ik4DLYS 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
1ik4ELYS 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
1ik4FLYS 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
ReferencesSectionsNo. of steps in catalysis
[1]Fig.7b, p.100842
[2]Fig.13
[3]eq 1, Fig.5a, Fig.7, p.2954-29582
[4]Fig.12, Fig.13, p.6815-68175
[6]Scheme 1

references
[1]
CommentsMUTAGENESIS OF ASPARTIC ACID RESIDUES.
Medline ID98332530
PubMed ID9665712
JournalBiochemistry
Year1998
Volume37
Pages10074-86
AuthorsSaadat D, Harrison DH
TitleIdentification of catalytic bases in the active site of Escherichia coli methylglyoxal synthase: cloning, expression, and functional characterization of conserved aspartic acid residues.
Related Swiss-protP0A731
[2]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
Medline ID99197296
PubMed ID10368300
JournalStructure Fold Des
Year1999
Volume7
Pages309-17
AuthorsSaadat D, Harrison DH
TitleThe crystal structure of methylglyoxal synthase from Escherichia coli.
Related PDB1b93
Related Swiss-protP0A731
[3]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID20181667
PubMed ID10715115
JournalBiochemistry
Year2000
Volume39
Pages2950-60
AuthorsSaadat D, Harrison DH
TitleMirroring perfection: the structure of methylglyoxal synthase complexed with the competitive inhibitor 2-phosphoglycolate.
Related PDB1egh
Related Swiss-protP0A731
[4]
PubMed ID11389594
JournalBiochemistry
Year2001
Volume40
Pages6805-18
AuthorsMarks GT, Harris TK, Massiah MA, Mildvan AS, Harrison DH
TitleMechanistic implications of methylglyoxal synthase complexed with phosphoglycolohydroxamic acid as observed by X-ray crystallography and NMR spectroscopy.
Related PDB1ik4
[5]
PubMed ID12405831
JournalJ Am Chem Soc
Year2002
Volume124
Pages13047-52
AuthorsRose IA, Nowick JS
TitleMethylglyoxal synthetase, enol-pyruvaldehyde, glutathione and the glyoxalase system.
[6]
PubMed ID12475328
JournalJ Am Chem Soc
Year2002
Volume124
Pages14871-8
AuthorsZhang X, Harrison DH, Cui Q
TitleFunctional specificities of methylglyoxal synthase and triosephosphate isomerase: a combined QM/MM analysis.

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.

createdupdated
2004-06-282009-02-26


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 2010)
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)

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