1. 1 Chapter 12 Zinc  Lewis Acid and Gene Regulator Copyright © 2012 Elsevier Inc. All rights reserved.

2. 2 FIGURE 12.1 Zinc-binding sites in enzymes can be catalytic, structural, or cocatalytic. The protein ligands are indicated by smaller filled circles.

3. 3 Copyright © 2012 Elsevier Inc. All rights reserved. FIGURE 12.2 The zinc-bound water can either be ionised to zinc-bound hydroxide, polarised by a general base to generate a nucleophile for catalysis or displaced by the substrate.

4. 4 Copyright © 2012 Elsevier Inc. All rights reserved. FIGURE 12.3 The active site of human carbonic anhydrase.

5. 5 Copyright © 2012 Elsevier Inc. All rights reserved. FIGURE 12.4 The main features of the mechanism of carbonic anhydrase.

6. 6 Copyright © 2012 Elsevier Inc. All rights reserved. FIGURE 12.5 Active sites of thermolysin and carboxypeptidases A and B.

7. 7 Copyright © 2012 Elsevier Inc. All rights reserved. FIGURE 12.6 Two possible reaction pathways for carboxypeptidase A. (Adapted from Wu et al., 2010.)

8. 8 Copyright © 2012 Elsevier Inc. All rights reserved. FIGURE 12.7 MMP catalytic domain structure. (a) Stereographic Richardson plot of the catalytic domain of human MMP-8 (Phe79eGly242) shown in standard orientation (PDB 1JAN). The repetitive secondary structure elements (orange arrows for  -strands,  I  V; cyan ribbons for  -helices,  A  C) and the four cations (two zinc ions in magenta and two calcium ions in red) are depicted. The side chains of the zinc-binding histidines, the general base/acid glutamate, the Met-turn methionine, and residues engaged in key electrostatic interactions (grey dots) within the C-terminal subdomain are shown as stick models with yellow carbons and labeled. A substrate of sequence Pro  Leu  Gly  Leu  Ala, modeled based on published inhibitor structures, is shown as a stick model with grey carbons. Additional relevant chain segments are shown in distinct colours and labeled (Met-turn in green; specificity loop in red; S10-wall-forming segment in blue; S-loop in purple; and bulge-edge segment in magenta). (b) Topology scheme of MMP-8 in the same orientation as in (A). (c) Close-up view of (A) depicting the side chains engaged in zinc-binding and those shaping the specificity pocket, which are labeled. (From Tallant, Marrero, & Gomis-Ru¨th, 2010. Copyright 2010 with permission from Elsevier.)

9. 9 Copyright © 2012 Elsevier Inc. All rights reserved. FIGURE 12.8 Catalytic mechanism of MMPs. Scheme for the cleavage mechanism proposed for MMPs, with the catalytic zinc ion as a sphere and hydrogen bonds as dashed lines. The three histidine ligands are represented by sticks. One conceivable alternative is that the second proton is transferred directly from the gem-diolate to the leaving amine in II and not via the general base/acid glutamate. This proton transfer could hypothetically occur before or after scissile-bond cleavage. (Adapted from Tallant et al., 2010.)

10. 10 Copyright © 2012 Elsevier Inc. All rights reserved. FIGURE 12.9 Reactions catalysed by SDR enzymes. (Adapted from Kavanagh, O¨rnvall, Persson, & Oppermann, 2008.)

11. 11 Copyright © 2012 Elsevier Inc. All rights reserved. FIGURE 12.10 The essential features of the catalytic cycle of liver alcohol dehydrogenase. (Adapted from Parkin, 2004.)

12. 12 Copyright © 2012 Elsevier Inc. All rights reserved. FIGURE 12.11 Specific attachment of a prochiral centre to an enzyme-binding site enables the enzyme to distinguish between prochiral methylene protons in ethanol. (Adapted from Voet & Voet, 2004.)

13. 13 Copyright © 2012 Elsevier Inc. All rights reserved. FIGURE 12.12 Some other active site coordination motifs in mononuclear zinc enzymes: from left to right bacteriophage T7 lysozyme, 5-aminolaevulinate dehydratase, Ada DNA repair protein. (Adapted from Parkin, 2004.)

14. 14 Copyright © 2012 Elsevier Inc. All rights reserved. FIGURE 12.13 Repair of damaged DNA by sacrificial alkylation of one of the zinc cysteine thiolate ligands of the Ada DNA repair protein. (Adapted from Parkin, 2004.)

15. 15 Copyright © 2012 Elsevier Inc. All rights reserved. FIGURE 12.14 The zinc-binding sites of subclass B1 (BCII from B cereus), B2 (CphA from A. hydrophila), and B3 (FEZ1 L. gormanii)  -lactamases. (From Bebrone, 2007. Copyright 2007 with permission from Elsevier.)

16. 16 Copyright © 2012 Elsevier Inc. All rights reserved. FIGURE 12.15 Drawings of the active sites of the leucine aminopeptidases BlLAP (Protein Data Bank [PDB]: 1LAM), AAP (PDB: 1AMP), and SAP (PDB: 1CP7) based on X-ray crystallography. (Adapted from Holz, Bzymek, & Swierczek, 2003.)

17. 17 Copyright © 2012 Elsevier Inc. All rights reserved. FIGURE 12.16 Proposed general mechanism for the hydrolysis of a peptide, catalysed by a metallopeptidase with a cocatalytic active site where R1, R2, R3 are substrate side chains and R is an N- terminal amine or a C-terminal carboxylate. This mechanism is based on the proposed mechanism for the aminopeptidase from Aeromonas proteolytica. (Adapted from Holz et al., 2003.)

18. 18 Copyright © 2012 Elsevier Inc. All rights reserved. FIGURE 12.17 Metal coordination sites in trinuclear zinc enzymes. (Adapted from Parkin, 2004.)

19. 19 Copyright © 2012 Elsevier Inc. All rights reserved. FIGURE 12.18 Coordination of the dinuclear site in kidney bean purple acid phosphatase. (Adapted from Parkin, 2004.)

20. 20 Copyright © 2012 Elsevier Inc. All rights reserved. FIGURE 12.19 (Left) Schematic representation of tandemly repeated zinc finger motif with their tetrahedrally coordinated Zn 2+ ions. Conserved amino acids are labeled and the most probable DNA- binding side chains are indicated by balls. (Right) A ribbon diagram of a single zinc finger motif in a ribbon diagram representation. (From Voet & Voet, 2004. Copyright 2004 with permission from John Wiley and Sons.)

21. 21 Copyright © 2012 Elsevier Inc. All rights reserved. FIGURE 12.20 (a) TFIIIA binds to 5S rRNA promoter sequences using zinc fingers 1  3, 5, and 7  9 which recognise respectively box C (green), the IE sequences (red), and box A (orange). (b) TFIIIA binds to 5S rRNA using primarily zinc fingers 4  6. Finger 4 binds to sequences in loop E, finger 5 to backbone atoms in helix V, and finger 6 binds to sequences in loop A. (From Hall, 2005. Copyright 2005 with permission from Elsevier.)

22. 22 Copyright © 2012 Elsevier Inc. All rights reserved. FIGURE 12.21 DNA and RNA recognition by the fifth zinc finger of TFIIIA. (a) The zinc finger recognises bases in the major groove of 5S rRNA promoter DNA (b) The finger recognises the phosphate groups of 5S rRNA. (From Hall, 2005. Copyright 2005 with permission from Elsevier.)

23. 23 Copyright © 2012 Elsevier Inc. All rights reserved. UnnFIGURE 12.1