EzCatDB: S00185
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DB codeS00185
RLCP classification8.131.705800.452 : Isomerization
8.113.585900.479 : Isomerization
CATH domainDomain 13.10.180.10 : 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1Catalytic domain
E.C.4.4.1.5
CSA1fro
MACiEM0032

CATH domainRelated DB codes (homologues)
3.10.180.10 : 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1D00446,D00447,D00448,S00540

Enzyme Name
UniProtKBKEGG

Q04760
Protein nameLactoylglutathione lyaselactoylglutathione lyase
methylglyoxalase
aldoketomutase
ketone-aldehyde mutase
glyoxylase I
(R)-S-lactoylglutathione methylglyoxal-lyase (isomerizing)
SynonymsEC 4.4.1.5
Methylglyoxalase
Aldoketomutase
Glyoxalase I
Glx I
Ketone-aldehyde mutase
S-D-lactoylglutathione methylglyoxal lyase
RefSeqNP_006699.2 (Protein)
NM_006708.2 (DNA/RNA sequence)
PfamPF00903 (Glyoxalase)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00620Pyruvate metabolism

UniProtKB:Accession NumberQ04760
Entry nameLGUL_HUMAN
Activity(R)-S-lactoylglutathione = glutathione + methylglyoxal.
SubunitHomodimer.
Subcellular location
CofactorBinds 1 zinc ion per subunit.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProductsintermediates
KEGG-idC00038C00051C00546C03451I00019I00020
CompoundZincGlutathioneMethylglyoxal(R)-S-LactoylglutathioneS-hemithiolacetal-glutathioneS-enediol-glutathione
Typeheavy metalamino acids,carboxyl group,peptide/protein,sulfhydryl groupcarbohydrateamino acids,carbohydrate,carboxyl group,sulfide group,peptide/protein

ChEBI29105
16856
17158
15694


PubChem32051
25246407
124886
880
440018


              
1bh5ABound:_ZNUnboundUnboundAnalogue:GTXUnboundUnbound
1bh5BBound:_ZNUnboundUnboundAnalogue:GTXUnboundUnbound
1bh5CBound:_ZNUnboundUnboundAnalogue:GTXUnboundUnbound
1bh5DBound:_ZNUnboundUnboundAnalogue:GTXUnboundUnbound
1froABound:_ZNUnboundUnboundAnalogue:GSBUnboundUnbound
1froBBound:_ZNUnboundUnboundAnalogue:GSBUnboundUnbound
1froCBound:_ZNUnboundUnboundAnalogue:GSBUnboundUnbound
1froDBound:_ZNUnboundUnboundAnalogue:GSBUnboundUnbound
1qinABound:_ZNUnboundUnboundUnboundUnboundIntermediate-analogue:GIP
1qinBBound:_ZNUnboundUnboundUnboundUnboundIntermediate-analogue:GIP
1qipABound:_ZNUnboundUnboundAnalogue:GNBUnboundUnbound
1qipBBound:_ZNUnboundUnboundAnalogue:GNBUnboundUnbound
1qipCBound:_ZNUnboundUnboundAnalogue:GNBUnboundUnbound
1qipDBound:_ZNUnboundUnboundAnalogue:GNBUnboundUnbound

Active-site residues
resource
Swiss-prot;Q59384, Q04760 & PDB;1fro & literature [28]
pdbCatalytic residuesCofactor-binding residuescomment
           
1bh5AGLU 99;       
      ;GLU 99;HIS 126;       (Zinc binding)
mutant Q33E,E172Q
1bh5BGLU 99;       
      ;GLU 99;HIS 126;       (Zinc binding)
mutant Q33E,E172Q
1bh5CGLU 99;       
      ;GLU 99;HIS 126;       (Zinc binding)
mutant Q33E,E172Q
1bh5DGLU 99;       
      ;GLU 99;HIS 126;       (Zinc binding)
mutant Q33E,E172Q
1froAGLU 99;GLU 172
GLN 33;GLU 99;HIS 126;GLU 172(Zinc binding)
 
1froBGLU 99;GLU 172
GLN 33;GLU 99;HIS 126;GLU 172(Zinc binding)
 
1froCGLU 99;GLU 172
GLN 33;GLU 99;HIS 126;GLU 172(Zinc binding)
 
1froDGLU 99;GLU 172
GLN 33;GLU 99;HIS 126;GLU 172(Zinc binding)
 
1qinAGLU 99;GLU 172
GLN 33;GLU 99;HIS 126;GLU 172(Zinc binding)
 
1qinBGLU 99;GLU 172
GLN 33;GLU 99;HIS 126;GLU 172(Zinc binding)
 
1qipAGLU 99;GLU 172
GLN 33;GLU 99;HIS 126;GLU 172(Zinc binding)
 
1qipBGLU 99;GLU 172
GLN 33;GLU 99;HIS 126;GLU 172(Zinc binding)
 
1qipCGLU 99;GLU 172
GLN 33;GLU 99;HIS 126;GLU 172(Zinc binding)
 
1qipDGLU 99;GLU 172
GLN 33;GLU 99;HIS 126;GLU 172(Zinc binding)
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]Fig.6, p.4856-4857
[2]Fig.6, p.100292
[16]Fig.5, p.33903
[19]Fig.3, p.21626-216283
[20]Fig.12
[22]Fig.6, p.13488-134892
[23]p.93-94
[24]p.8725-8726
[28]Scheme 9, Scheme 133
[30]Scheme 3, Scheme 4, p.10284-102894
[31]Fig.4, p.69793

references
[1]
PubMed ID7138835
JournalBiochemistry
Year1982
Volume21
Pages4850-7
AuthorsSellin S, Eriksson LE, Mannervik B
TitleFluorescence and nuclear relaxation enhancement studies of the binding of glutathione derivatives to manganese-reconstituted glyoxalase I from human erythrocytes. A model for the catalytic mechanism of the enzyme involving a hydrated metal ion.
[2]
PubMed ID7107595
JournalJ Biol Chem
Year1982
Volume257
Pages10023-9
AuthorsSellin S, Rosevear PR, Mannervik B, Mildvan AS
TitleNuclear relaxation studies of the role of the essential metal in glyoxalase I.
[3]
PubMed ID6853506
JournalJ Biol Chem
Year1983
Volume258
Pages6823-6
AuthorsRosevear PR, Chari RV, Kozarich JW, Sellin S, Mannervik B, Mildvan AS
Title13C NMR studies of the product complex of glyoxalase I.
[4]
PubMed ID6296126
JournalJ Biol Chem
Year1983
Volume258
Pages2091-3
AuthorsSellin S, Eriksson LE, Aronsson AC, Mannervik B
TitleOctahedral metal coordination in the active site of glyoxalase I as evidenced by the properties of Co(II)-glyoxalase I.
[5]
PubMed ID6547959
JournalJ Biol Chem
Year1984
Volume259
Pages11436-47
AuthorsRosevear PR, Sellin S, Mannervik B, Kuntz ID, Mildvan AS
TitleNMR and computer modeling studies of the conformations of glutathione derivatives at the active site of glyoxalase I.
[6]
PubMed ID2827734
JournalBiochemistry
Year1987
Volume26
Pages6779-84
AuthorsSellin S, Eriksson LE, Mannervik B
TitleElectron paramagnetic resonance study of the active site of copper-substituted human glyoxalase I.
[7]
PubMed ID2226450
JournalEur J Biochem
Year1990
Volume193
Pages83-90
AuthorsRae C, Berners-Price SJ, Bulliman BT, Kuchel PW
TitleKinetic analysis of the human erythrocyte glyoxalase system using 1H NMR and a computer model.
[8]
PubMed ID1755849
JournalBiochem Biophys Res Commun
Year1991
Volume181
Pages657-63
AuthorsLi J, Guha MK, Creighton DJ
TitleEnzyme chemistry of dithiohemiacetals: synthesis and characterization of S-D-dithiomandeloylglutathione as an alternate substrate for glyoxalase I.
[9]
PubMed ID2043110
JournalBiochem Biophys Res Commun
Year1991
Volume177
Pages252-8
AuthorsXie XF, Creighton DJ
TitleSynthesis and initial characterization of gamma-L-glutamyl-L-thiothreonylglycine and gamma-L-glutamyl-L-allo-thiothreonylglycine as steric probes of the active site of glyoxalase I.
[10]
PubMed ID1472100
JournalBiochem Pharmacol
Year1992
Volume44
Pages2357-63
AuthorsLo TW, Thornalley PJ
TitleInhibition of proliferation of human leukaemia 60 cells by diethyl esters of glyoxalase inhibitors in vitro.
[11]
PubMed ID1627549
JournalBiochemistry
Year1992
Volume31
Pages6069-77
AuthorsLandro JA, Brush EJ, Kozarich JW
TitleIsomerization of (R)- and (S)-glutathiolactaldehydes by glyoxalase I: the case for dichotomous stereochemical behavior in a single active site.
[12]
PubMed ID1390924
JournalBiochim Biophys Acta
Year1992
Volume1159
Pages203-8
AuthorsHamilton DS, Creighton DJ
TitleCaution: the glycylmethyl and glycylethyl esters of glutathione are substrates for glyoxalase I.
[13]
PubMed ID1459997
JournalJ Biol Chem
Year1992
Volume267
Pages24933-6
AuthorsHamilton DS, Creighton DJ
TitleInhibition of glyoxalase I by the enediol mimic S-(N-hydroxy-N-methylcarbamoyl)glutathione. The possible basis of a tumor-selective anticancer strategy.
[14]
PubMed ID8359522
JournalBiochem Soc Trans
Year1993
Volume21
Pages515-7
AuthorsMannervik B, Ridderstrom M
TitleCatalytic and molecular properties of glyoxalase I.
[15]
PubMed ID8142352
JournalBiochemistry
Year1994
Volume33
Pages3548-59
AuthorsRae C, O'Donoghue SI, Bubb WA, Kuchel PW
TitleStereospecificity of substrate usage by glyoxalase 1: nuclear magnetic resonance studies of kinetics and hemithioacetal substrate conformation.
[16]
CommentsX-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
Medline ID97361820
PubMed ID9218781
JournalEMBO J
Year1997
Volume16
Pages3386-95
AuthorsCameron AD, Olin B, Ridderstrom M, Mannervik B, Jones TA
TitleCrystal structure of human glyoxalase I--evidence for gene duplication and 3D domain swapping.
Related PDB1fro
Related UniProtKBQ04760
[17]
PubMed ID9671502
JournalBiochemistry
Year1998
Volume37
Pages10345-53
AuthorsSaint-Jean AP, Phillips KR, Creighton DJ, Stone MJ
TitleActive monomeric and dimeric forms of Pseudomonas putida glyoxalase I: evidence for 3D domain swapping.
[18]
PubMed ID9871526
JournalBioorg Med Chem Lett
Year1998
Volume8
Pages705-10
AuthorsLy HD, Clugston SL, Sampson PB, Honek JF
TitleSyntheses and kinetic evaluation of hydroxamate-based peptide inhibitors of glyoxalase I.
[19]
CommentsX-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
Medline ID98370994
PubMed ID9705294
JournalJ Biol Chem
Year1998
Volume273
Pages21623-8
AuthorsRidderstrom M, Cameron AD, Jones TA, Mannervik B
TitleInvolvement of an active-site Zn2+ ligand in the catalytic mechanism of human glyoxalase I.
Related PDB1bh5
Related UniProtKBQ04760
[20]
PubMed ID9689946
JournalJ Theor Biol
Year1998
Volume193
Pages91-8
AuthorsKalapos MP
TitleFrom mineral support to enzymatic catalysis--further assumptions for the evolutionary history of glyoxalase system.
[21]
PubMed ID10082363
JournalProtein Sci
Year1998
Volume7
Pages1661-70
AuthorsBergdoll M, Eltis LD, Cameron AD, Dumas P, Bolin JT
TitleAll in the family: structural and evolutionary relationships among three modular proteins with diverse functions and variable assembly.
[22]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID99452689
PubMed ID10521255
JournalBiochemistry
Year1999
Volume38
Pages13480-90
AuthorsCameron AD, Ridderstrom M, Olin B, Kavarana MJ, Creighton DJ, Mannervik B
TitleReaction mechanism of glyoxalase I explored by an X-ray crystallographic analysis of the human enzyme in complex with a transition state analogue.
Related PDB1qin,1qip
Related UniProtKBQ04760
[23]
PubMed ID10403382
JournalFEBS Lett
Year1999
Volume453
Pages90-4
AuthorsFeierberg I, Cameron AD, Aqvist J
TitleEnergetics of the proposed rate-determining step of the glyoxalase I reaction.
[24]
CommentsX-RAY CRYSTALLOGRAPHY.
Medline ID20374551
PubMed ID10913283
JournalBiochemistry
Year2000
Volume39
Pages8719-27
AuthorsHe MM, Clugston SL, Honek JF, Matthews BW
TitleDetermination of the structure of Escherichia coli glyoxalase I suggests a structural basis for differential metal activation.
Related PDB1f9z,1fa5,1fa6,1fa7,1fa8
Related UniProtKBQ59384
[25]
PubMed ID10801792
JournalJ Biol Chem
Year2000
Volume275
Pages22657-62
AuthorsFeierberg I, Luzhkov V, Aqvist J
TitleComputer simulation of primary kinetic isotope effects in the proposed rate-limiting step of the glyoxalase I catalyzed reaction.
[26]
PubMed ID11052803
JournalJ Med Chem
Year2000
Volume43
Pages3981-6
AuthorsKalsi A, Kavarana MJ, Lu T, Whalen DL, Hamilton DS, Creighton DJ
TitleRole of hydrophobic interactions in binding S-(N-aryl/alkyl-N-hydroxycarbamoyl)glutathiones to the active site of the antitumor target enzyme glyoxalase I.
[27]
PubMed ID11212839
JournalJ Protein Chem
Year2000
Volume19
Pages389-97
AuthorsStokvis E, Clugston SL, Honek JF, Heck AJ
TitleCharacterization of glyoxalase I (E. coli)-inhibitor interactions by electrospray time-of-flight mass spectrometry and enzyme kinetic analysis.
[28]
PubMed ID11368170
JournalArch Biochem Biophys
Year2001
Volume387
Pages1-10
AuthorsCreighton DJ, Hamilton DS
TitleBrief history of glyoxalase I and what we have learned about metal ion-dependent, enzyme-catalyzed isomerizations.
[29]
PubMed ID11453985
JournalEur J Biochem
Year2001
Volume268
Pages3930-6
AuthorsMartins AM, Mendes P, Cordeiro C, Freire AP
TitleIn situ kinetic analysis of glyoxalase I and glyoxalase II in Saccharomyces cerevisiae.
[30]
PubMed ID11603978
JournalJ Am Chem Soc
Year2001
Volume123
Pages10280-9
AuthorsHimo F, Siegbahn PE
TitleCatalytic mechanism of glyoxalase I: a theoretical study.
[31]
PubMed ID11459475
JournalJ Am Chem Soc
Year2001
Volume123
Pages6973-82
AuthorsRichter U, Krauss M
TitleActive site structure and mechanism of human glyoxalase I-an ab initio theoretical study.
[32]
PubMed ID11050082
JournalJ Biol Chem
Year2001
Volume276
Pages1845-9
AuthorsFrickel EM, Jemth P, Widersten M, Mannervik B
TitleYeast glyoxalase I is a monomeric enzyme with two active sites.
[33]
PubMed ID11853416
JournalJ Am Chem Soc
Year2002
Volume124
Pages1564-5
AuthorsDiaconu D, Hu Z, Gorun SM
TitleCopper-based bioinspired oxygenation and glyoxalase-like reactivity.
[34]
PubMed ID12405831
JournalJ Am Chem Soc
Year2002
Volume124
Pages13047-52
AuthorsRose IA, Nowick JS
TitleMethylglyoxal synthetase, enol-pyruvaldehyde, glutathione and the glyoxalase system.

comments
These enzymes from human and other mammal utilizes zinc ion as a cofactor, whereas the counterpart enzymes from bacteria such as E. coli (S00540 in EzCatDB) use nickel ion as a cofactor. The octahedral coordination of metal ion is essential (see [24] and [28]).
This enzyme catalyzes the following reactions:
(A) Addition of sulfhydryl group of glutathione to carbonyl group of methylglyoxal, forming an intermediate, hemimercaptal- or hemithioacetal-glutathione (non-enzymatic reaction):
(B) Isomerization; Shift of double-bond from O=C-C to O-C=C, forming an enediol intermediate:
(C) Isomerization; Shift of double-bond from C=C-O to C-C=O:
According to the literature [28] and [30], the catalytic reactions for the S-enantiomer intermediate and the R-enantiomer must be different. As for the reaction for the R-enantiomer, two different mechanisms have been proposed, a "nondissociative" mechanism and a "dissociative" mechanism (see [28]).
As for the S-enantiomer reaction, the reaction proceeds as follows (see [28] and [31]).
(B) Isomerization; Shift of double-bond from O=C-C to O-C=C, forming an enediol intermediate:
(B1) The carbonyl group (O2) and hydroxyl group (O1) of the hemiacetal intermediate are bound to zinc ion. This coordination decrease the pKa of C1-H of the intermediate, facilitating its dissociation by a general base. (In contrast, Glu172 is displaced from the zinc ion, having its own pKa value increased.)
(B2) Glu172 acts as a general base to deprotonate C1-H, forming an enediolate.
(C) Isomerization; Shift of double-bond from C=C-O to C-C=O:
(C1) Glu172 acts as a general acid to protonate the C2 carbon, whereas Glu99 acts as a general base to deprotonate the O1 hydroxyl group.
(C2) Glu99 acts as a general acid to protonate the O2 oxygen, completing the reaction.
For the R-enantiomer reaction, the dissociative reaction proceeds as follows (see [30]):
(B') Isomerization; Shift of double-bond from O=C-C to O-C=C, forming an enediol intermediate:
(B'1) The carbonyl group (O2) and hydroxyl group (O1) of the hemiacetal intermediate are bound to zinc ion. This coordination decrease the pKa of C1-H of the intermediate, facilitating its dissociation by a general base.
(B'2) Glu99 acts as a general base to deprotonate C1-H.
(B'2) Glu99 acts as a general acid to protonate O2, forming an enediol intermediate.
(C') Isomerization; Shift of double-bond from C=C-O to C-C=O:
(C'1) Glu172 acts as a general base to deprotonate the O1 hydroxyl group.
(C'2) Glu172 acts as a general acid to protonate the C2 carbon, completing the reaction.
For the R-enantiomer reaction, the nondissociative reaction proceeds as follows (see [28]):
(X) Elimination of glutathione from the R-enantiomer, forming an aldehyde intermediate:
(Y) Addition of glutathione to the aldehyde intermediate, forming a S-enantiomer:
After the formation of the S-enantiomer, the reaction follows the above reaction mechanisms, (B) and (C).
However, it is not clear which of the reaction mechanisms for the R-enantiomer is adopted by this enzyme.

createdupdated
2004-05-272010-01-21


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 - )
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