Volume 7, Issue 9, Pages 1067-1078 (September 1999) Crystal structure of human glyoxalase II and its complex with a glutathione thiolester substrate analogue  Alexander D Cameron, Marianne Ridderström, Birgit Olin, Bengt Mannervik  Structure  Volume 7, Issue 9, Pages 1067-1078 (September 1999) DOI: 10.1016/S0969-2126(99)80174-9

Figure 1 The glyoxalase system. GSH represents reduced glutathione (γ-L-Glu-L-Cys-Gly). Structure 1999 7, 1067-1078DOI: (10.1016/S0969-2126(99)80174-9)

Figure 2 Overall structure of glyoxalase II and a comparison with the metallo-β-lactamase. (a) Schematic representation of glyoxalase II. The molecule has been colour ramped according to residue number starting with red at the N terminus and finishing with blue at the C terminus. The β strands of the first domain and the α helices of the second domain have been labelled for clarity. The metal ions and the coordinating residues are represented by balls and sticks. The figure was prepared using MolScript version 2.1 [54]. (b) Similar view of the metallo-β-lactamase from B. fragilis [16] after it had been superimposed on glyoxalase II. (c) Topology diagram of glyoxalase II. The approximate position of the twofold axis relating the two halves of the β sheet is indicated. The numbering shows the N and C termini, respectively, of each secondary structure element. The secondary structural elements were defined using the YASSPA algorithm implemented in O [45]. Structure 1999 7, 1067-1078DOI: (10.1016/S0969-2126(99)80174-9)

Figure 3 Stereoview of the electron density in the active site of the HBPC–GSH complex. The density is calculated with coefficients 2mFobs–dFcalc using the final structure and contoured at 1σ. The ligand is shown with orange carbon atoms and protein residues are shown with khaki carbon atoms. Although the density for the phenyl group is poor, it is clear how the ligand binds. The γ-glutamate of the HBPC–GSH is not shown beyond the carbonyl oxygen. The figure was prepared in O. Structure 1999 7, 1067-1078DOI: (10.1016/S0969-2126(99)80174-9)

Figure 4 Metal coordination in glyoxalase II. (a) The complex with cacodylate. (b) The molecule with GSH bound. (c) The molecule with HBPC–GSH bound. The protein residues are shown with brown carbon atoms and the ligands with red carbon atoms. Only the Cα, Cβ and S atoms of the cysteine moiety of the GSH and HBPC–GSH are shown. The figure was generated in MolScript version 2.1 [54] and rendered in Raster3D [55]. Structure 1999 7, 1067-1078DOI: (10.1016/S0969-2126(99)80174-9)

Figure 5 View of the active site in glyoxalase II. (a) Residues coordinating the zinc ion or those within hydrogen-bonding distance of the HBPC–GSH are represented as balls and sticks with yellow carbon atoms. The HBPC–GSH is shown as a ball-and-stick representation with orange carbon atoms. The surrounding schematic view of the backbone is coloured as in Figure 2a. The HBPC–GSH is truncated as in Figure 3. (b) Schematic diagram showing the interactions between the HBPC–GSH and the protein. The ligand is shown with purple bonds and the protein residues with brown bonds. Atoms and residues involved in hydrophobic contacts are shown as fanned by red dashes. The figure was made using LIGPLOT [56]. Structure 1999 7, 1067-1078DOI: (10.1016/S0969-2126(99)80174-9)

Figure 6 Sequence conservation among the glyoxalase II enzymes. The sequences were aligned using ClustalW [37]. Human, Homo sapiens, SWISS-PROT accession no. Q16775; Marmoset, Callithrix jacchus, SWISS-PROT accession no. Q28333; Rat, Rattus norvegicus GENBANK accession no. U97667; A. thaliana, Arabidopsis thaliana, EMBL accession no. Y08357; S_mansoni, Schistosoma mansoni, SWISS-PROT accession no. Q26547; C_elegans, Caenorhabditis elegans, EMBL accession no. AL023828; Yeast_glo2, Saccharomyces cerevisiae, SWISS-PROT accession no. Q05584; Yeast_glo4, Saccharomyces cerevisiae, SWISS-PROT accession no. Q12320; R_capsulatus, Rhodobacter capsulatus, EMBL accession no. X99599; R_blasticus, Rhodobacter blasticus, SWISS-PROT accession no. P05446; A_thaliana_mit, Arabidopsis thaliana, GENBANK accession no. U90927 (mitochondrial); E_coli, Escherichia coli, SWISS-PROT accession no. Q47677; B_aphidicola, Buchnera aphidicola, SWISS-PROT accession no. Q08889; Synechocystis, Synechocystis PCC6803, SWISS-PROT accession no. P72933; S_pombe, Schizosaccharomyces pombe, EMBL accession no. AL032681; H_influenzae, Haemophilus influenzae, SWISS-PROT accession no. P71374. Numbering corresponds to the human enzyme. The secondary structure is as shown in Figure 2. Vertical lines indicate the ends of the two β sheets of the sandwich. Residues that are identical to at least 14 out of the other 15 matched residues are coloured red and those identical to more than 11, blue. Residues that are conserved but not identical are coloured green. Conservation was calculated in ALSCRIPT [57] with a value of 6. The residues that coordinate zincs 1, 2 or both are denoted by Z1, Z2 and ZB, respectively. Residues within hydrogen-bonding distance of the GSH are shown by G. GM denotes that the glutathione interacts with the mainchain of the residue. Structure 1999 7, 1067-1078DOI: (10.1016/S0969-2126(99)80174-9)

Figure 7 Stereoview of glyoxalase II coloured according to conservation as shown for the glyoxalase sequence in Figure 6. The metal ions and the coordinating residues are shown. The HBPC–GSH is shown in orange. The figure was prepared in ALSCRIPT. Structure 1999 7, 1067-1078DOI: (10.1016/S0969-2126(99)80174-9)

Figure 8 A reaction mechanism for glyoxalase II proposed on the basis of the position of HBPC–GSH in the active site. GSH represents reduced glutathione (γ-L-Glu-L-Cys-Gly). The hydroxide ion is next to the carbonyl carbon, zinc 1 close to the carbonyl oxygen and zinc 2 near the sulphur of the HBPC–GSH. The hydroxide attacks the carbonyl carbon to form a negatively tetrahedral intermediate that may be stabilised by coordination to zinc 1. The C–S bond then breaks to yield the product. Presumably, in the apo enzyme, the sixth coordination positions of the zinc ions will be taken up by water molecules but these are not shown in the diagram. Structure 1999 7, 1067-1078DOI: (10.1016/S0969-2126(99)80174-9)