DB code: S00185

RLCP classification 8.131.705800.452 : Isomerization
8.113.585900.479 : Isomerization
CATH domain 3.10.180.10 : 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 Catalytic domain
E.C. 4.4.1.5
CSA 1fro
M-CSA 1fro
MACiE M0032

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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
Q04760 Lactoylglutathione lyase
EC 4.4.1.5
Methylglyoxalase
Aldoketomutase
Glyoxalase I
Glx I
Ketone-aldehyde mutase
S-D-lactoylglutathione methylglyoxal lyase
NP_006699.2 (Protein)
NM_006708.2 (DNA/RNA sequence)
PF00903 (Glyoxalase)
[Graphical View]

KEGG enzyme name
lactoylglutathione lyase
methylglyoxalase
aldoketomutase
ketone-aldehyde mutase
glyoxylase I
(R)-S-lactoylglutathione methylglyoxal-lyase (isomerizing)

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q04760 LGUL_HUMAN (R)-S-lactoylglutathione = glutathione + methylglyoxal. Homodimer. Binds 1 zinc ion per subunit.

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

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00038 C00051 C00546 C03451 I00019 I00020
E.C.
Compound Zinc Glutathione Methylglyoxal (R)-S-Lactoylglutathione S-hemithiolacetal-glutathione S-enediol-glutathione
Type heavy metal amino acids,carboxyl group,peptide/protein,sulfhydryl group carbohydrate amino acids,carbohydrate,carboxyl group,sulfide group,peptide/protein
ChEBI 29105
16856
17158
15694
PubChem 32051
124886
25246407
880
440018
1bh5A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Analogue:GTX Unbound Unbound
1bh5B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Analogue:GTX Unbound Unbound
1bh5C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Analogue:GTX Unbound Unbound
1bh5D Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Analogue:GTX Unbound Unbound
1froA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Analogue:GSB Unbound Unbound
1froB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Analogue:GSB Unbound Unbound
1froC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Analogue:GSB Unbound Unbound
1froD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Analogue:GSB Unbound Unbound
1qinA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound Intermediate-analogue:GIP
1qinB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound Intermediate-analogue:GIP
1qipA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Analogue:GNB Unbound Unbound
1qipB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Analogue:GNB Unbound Unbound
1qipC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Analogue:GNB Unbound Unbound
1qipD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Analogue:GNB Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;Q59384, Q04760 & PDB;1fro & literature [28]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1bh5A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 99; ;GLU 99;HIS 126; (Zinc binding) mutant Q33E,E172Q
1bh5B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 99; ;GLU 99;HIS 126; (Zinc binding) mutant Q33E,E172Q
1bh5C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 99; ;GLU 99;HIS 126; (Zinc binding) mutant Q33E,E172Q
1bh5D Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 99; ;GLU 99;HIS 126; (Zinc binding) mutant Q33E,E172Q
1froA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 99;GLU 172 GLN 33;GLU 99;HIS 126;GLU 172(Zinc binding)
1froB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 99;GLU 172 GLN 33;GLU 99;HIS 126;GLU 172(Zinc binding)
1froC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 99;GLU 172 GLN 33;GLU 99;HIS 126;GLU 172(Zinc binding)
1froD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 99;GLU 172 GLN 33;GLU 99;HIS 126;GLU 172(Zinc binding)
1qinA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 99;GLU 172 GLN 33;GLU 99;HIS 126;GLU 172(Zinc binding)
1qinB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 99;GLU 172 GLN 33;GLU 99;HIS 126;GLU 172(Zinc binding)
1qipA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 99;GLU 172 GLN 33;GLU 99;HIS 126;GLU 172(Zinc binding)
1qipB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 99;GLU 172 GLN 33;GLU 99;HIS 126;GLU 172(Zinc binding)
1qipC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 99;GLU 172 GLN 33;GLU 99;HIS 126;GLU 172(Zinc binding)
1qipD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 99;GLU 172 GLN 33;GLU 99;HIS 126;GLU 172(Zinc binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
Fig.6, p.4856-4857
[2]
Fig.6, p.10029 2
[16]
Fig.5, p.3390 3
[19]
Fig.3, p.21626-21628 3
[20]
Fig.1 2
[22]
Fig.6, p.13488-13489 2
[23]
p.93-94
[24]
p.8725-8726
[28]
Scheme 9, Scheme 13 3
[30]
Scheme 3, Scheme 4, p.10284-10289 4
[31]
Fig.4, p.6979 3

References
[1]
Resource
Comments
Medline ID
PubMed ID 7138835
Journal Biochemistry
Year 1982
Volume 21
Pages 4850-7
Authors Sellin S, Eriksson LE, Mannervik B
Title Fluorescence 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.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 7107595
Journal J Biol Chem
Year 1982
Volume 257
Pages 10023-9
Authors Sellin S, Rosevear PR, Mannervik B, Mildvan AS
Title Nuclear relaxation studies of the role of the essential metal in glyoxalase I.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 6853506
Journal J Biol Chem
Year 1983
Volume 258
Pages 6823-6
Authors Rosevear PR, Chari RV, Kozarich JW, Sellin S, Mannervik B, Mildvan AS
Title 13C NMR studies of the product complex of glyoxalase I.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 6296126
Journal J Biol Chem
Year 1983
Volume 258
Pages 2091-3
Authors Sellin S, Eriksson LE, Aronsson AC, Mannervik B
Title Octahedral metal coordination in the active site of glyoxalase I as evidenced by the properties of Co(II)-glyoxalase I.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 6547959
Journal J Biol Chem
Year 1984
Volume 259
Pages 11436-47
Authors Rosevear PR, Sellin S, Mannervik B, Kuntz ID, Mildvan AS
Title NMR and computer modeling studies of the conformations of glutathione derivatives at the active site of glyoxalase I.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 2827734
Journal Biochemistry
Year 1987
Volume 26
Pages 6779-84
Authors Sellin S, Eriksson LE, Mannervik B
Title Electron paramagnetic resonance study of the active site of copper-substituted human glyoxalase I.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 2226450
Journal Eur J Biochem
Year 1990
Volume 193
Pages 83-90
Authors Rae C, Berners-Price SJ, Bulliman BT, Kuchel PW
Title Kinetic analysis of the human erythrocyte glyoxalase system using 1H NMR and a computer model.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 1755849
Journal Biochem Biophys Res Commun
Year 1991
Volume 181
Pages 657-63
Authors Li J, Guha MK, Creighton DJ
Title Enzyme chemistry of dithiohemiacetals: synthesis and characterization of S-D-dithiomandeloylglutathione as an alternate substrate for glyoxalase I.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 2043110
Journal Biochem Biophys Res Commun
Year 1991
Volume 177
Pages 252-8
Authors Xie XF, Creighton DJ
Title Synthesis 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.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 1472100
Journal Biochem Pharmacol
Year 1992
Volume 44
Pages 2357-63
Authors Lo TW, Thornalley PJ
Title Inhibition of proliferation of human leukaemia 60 cells by diethyl esters of glyoxalase inhibitors in vitro.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 1627549
Journal Biochemistry
Year 1992
Volume 31
Pages 6069-77
Authors Landro JA, Brush EJ, Kozarich JW
Title Isomerization of (R)- and (S)-glutathiolactaldehydes by glyoxalase I: the case for dichotomous stereochemical behavior in a single active site.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 1390924
Journal Biochim Biophys Acta
Year 1992
Volume 1159
Pages 203-8
Authors Hamilton DS, Creighton DJ
Title Caution: the glycylmethyl and glycylethyl esters of glutathione are substrates for glyoxalase I.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 1459997
Journal J Biol Chem
Year 1992
Volume 267
Pages 24933-6
Authors Hamilton DS, Creighton DJ
Title Inhibition of glyoxalase I by the enediol mimic S-(N-hydroxy-N-methylcarbamoyl)glutathione. The possible basis of a tumor-selective anticancer strategy.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 8359522
Journal Biochem Soc Trans
Year 1993
Volume 21
Pages 515-7
Authors Mannervik B, Ridderstrom M
Title Catalytic and molecular properties of glyoxalase I.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 8142352
Journal Biochemistry
Year 1994
Volume 33
Pages 3548-59
Authors Rae C, O'Donoghue SI, Bubb WA, Kuchel PW
Title Stereospecificity of substrate usage by glyoxalase 1: nuclear magnetic resonance studies of kinetics and hemithioacetal substrate conformation.
Related PDB
Related UniProtKB
[16]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
Medline ID 97361820
PubMed ID 9218781
Journal EMBO J
Year 1997
Volume 16
Pages 3386-95
Authors Cameron AD, Olin B, Ridderstrom M, Mannervik B, Jones TA
Title Crystal structure of human glyoxalase I--evidence for gene duplication and 3D domain swapping.
Related PDB 1fro
Related UniProtKB Q04760
[17]
Resource
Comments
Medline ID
PubMed ID 9671502
Journal Biochemistry
Year 1998
Volume 37
Pages 10345-53
Authors Saint-Jean AP, Phillips KR, Creighton DJ, Stone MJ
Title Active monomeric and dimeric forms of Pseudomonas putida glyoxalase I: evidence for 3D domain swapping.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 9871526
Journal Bioorg Med Chem Lett
Year 1998
Volume 8
Pages 705-10
Authors Ly HD, Clugston SL, Sampson PB, Honek JF
Title Syntheses and kinetic evaluation of hydroxamate-based peptide inhibitors of glyoxalase I.
Related PDB
Related UniProtKB
[19]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
Medline ID 98370994
PubMed ID 9705294
Journal J Biol Chem
Year 1998
Volume 273
Pages 21623-8
Authors Ridderstrom M, Cameron AD, Jones TA, Mannervik B
Title Involvement of an active-site Zn2+ ligand in the catalytic mechanism of human glyoxalase I.
Related PDB 1bh5
Related UniProtKB Q04760
[20]
Resource
Comments
Medline ID
PubMed ID 9689946
Journal J Theor Biol
Year 1998
Volume 193
Pages 91-8
Authors Kalapos MP
Title From mineral support to enzymatic catalysis--further assumptions for the evolutionary history of glyoxalase system.
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 10082363
Journal Protein Sci
Year 1998
Volume 7
Pages 1661-70
Authors Bergdoll M, Eltis LD, Cameron AD, Dumas P, Bolin JT
Title All in the family: structural and evolutionary relationships among three modular proteins with diverse functions and variable assembly.
Related PDB
Related UniProtKB
[22]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID 99452689
PubMed ID 10521255
Journal Biochemistry
Year 1999
Volume 38
Pages 13480-90
Authors Cameron AD, Ridderstrom M, Olin B, Kavarana MJ, Creighton DJ, Mannervik B
Title Reaction mechanism of glyoxalase I explored by an X-ray crystallographic analysis of the human enzyme in complex with a transition state analogue.
Related PDB 1qin 1qip
Related UniProtKB Q04760
[23]
Resource
Comments
Medline ID
PubMed ID 10403382
Journal FEBS Lett
Year 1999
Volume 453
Pages 90-4
Authors Feierberg I, Cameron AD, Aqvist J
Title Energetics of the proposed rate-determining step of the glyoxalase I reaction.
Related PDB
Related UniProtKB
[24]
Resource
Comments X-RAY CRYSTALLOGRAPHY.
Medline ID 20374551
PubMed ID 10913283
Journal Biochemistry
Year 2000
Volume 39
Pages 8719-27
Authors He MM, Clugston SL, Honek JF, Matthews BW
Title Determination of the structure of Escherichia coli glyoxalase I suggests a structural basis for differential metal activation.
Related PDB 1f9z 1fa5 1fa6 1fa7 1fa8
Related UniProtKB Q59384
[25]
Resource
Comments
Medline ID
PubMed ID 10801792
Journal J Biol Chem
Year 2000
Volume 275
Pages 22657-62
Authors Feierberg I, Luzhkov V, Aqvist J
Title Computer simulation of primary kinetic isotope effects in the proposed rate-limiting step of the glyoxalase I catalyzed reaction.
Related PDB
Related UniProtKB
[26]
Resource
Comments
Medline ID
PubMed ID 11052803
Journal J Med Chem
Year 2000
Volume 43
Pages 3981-6
Authors Kalsi A, Kavarana MJ, Lu T, Whalen DL, Hamilton DS, Creighton DJ
Title Role of hydrophobic interactions in binding S-(N-aryl/alkyl-N-hydroxycarbamoyl)glutathiones to the active site of the antitumor target enzyme glyoxalase I.
Related PDB
Related UniProtKB
[27]
Resource
Comments
Medline ID
PubMed ID 11212839
Journal J Protein Chem
Year 2000
Volume 19
Pages 389-97
Authors Stokvis E, Clugston SL, Honek JF, Heck AJ
Title Characterization of glyoxalase I (E. coli)-inhibitor interactions by electrospray time-of-flight mass spectrometry and enzyme kinetic analysis.
Related PDB
Related UniProtKB
[28]
Resource
Comments
Medline ID
PubMed ID 11368170
Journal Arch Biochem Biophys
Year 2001
Volume 387
Pages 1-10
Authors Creighton DJ, Hamilton DS
Title Brief history of glyoxalase I and what we have learned about metal ion-dependent, enzyme-catalyzed isomerizations.
Related PDB
Related UniProtKB
[29]
Resource
Comments
Medline ID
PubMed ID 11453985
Journal Eur J Biochem
Year 2001
Volume 268
Pages 3930-6
Authors Martins AM, Mendes P, Cordeiro C, Freire AP
Title In situ kinetic analysis of glyoxalase I and glyoxalase II in Saccharomyces cerevisiae.
Related PDB
Related UniProtKB
[30]
Resource
Comments
Medline ID
PubMed ID 11603978
Journal J Am Chem Soc
Year 2001
Volume 123
Pages 10280-9
Authors Himo F, Siegbahn PE
Title Catalytic mechanism of glyoxalase I: a theoretical study.
Related PDB
Related UniProtKB
[31]
Resource
Comments
Medline ID
PubMed ID 11459475
Journal J Am Chem Soc
Year 2001
Volume 123
Pages 6973-82
Authors Richter U, Krauss M
Title Active site structure and mechanism of human glyoxalase I-an ab initio theoretical study.
Related PDB
Related UniProtKB
[32]
Resource
Comments
Medline ID
PubMed ID 11050082
Journal J Biol Chem
Year 2001
Volume 276
Pages 1845-9
Authors Frickel EM, Jemth P, Widersten M, Mannervik B
Title Yeast glyoxalase I is a monomeric enzyme with two active sites.
Related PDB
Related UniProtKB
[33]
Resource
Comments
Medline ID
PubMed ID 11853416
Journal J Am Chem Soc
Year 2002
Volume 124
Pages 1564-5
Authors Diaconu D, Hu Z, Gorun SM
Title Copper-based bioinspired oxygenation and glyoxalase-like reactivity.
Related PDB
Related UniProtKB
[34]
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

Comments
(C) Isomerization; Shift of double-bond from C=C-O to C-C=O:
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:
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.

Created Updated
2004-05-27 2010-01-21