1. Nickel and Cobalt: Evolutionary Relics
Chapter 15
Nickel and Cobalt: Evolutionary Relics
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FIGURE 15.1 The dinuclear Ni active site of urease. Ni atoms are shown in green, metal-bound water as red spheres; the carbamylated Lys is K217*. (From Mulrooney & Hausinger, Copyright 2003 with permission from Elsevier.)
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FIGURE 15.2 Structure of the NiFe active site and mechanism of hydrogenase. The structure is based on PDB code ICC1, while the mechanism of hydrogenase activation and catalysis is based on the work of Lill and Siegbahn (2009). The asterisks indicate an EPR-active state. (Adapted from Ragsdale, 2009.)
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FIGURE 15.3 The WoodLjungdahl pathway. “H2” is used in a general sense to designate the requirement for two electrons and two protons in the reaction. (From Ragsdale & Pierce, Copyright 2008 with permission from Elsevier.)
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FIGURE 15.4 The coupling of CODH activity with hydrogenase activity in R. rubrum. The two subunits of CPDH are shown with light and dark wire tracings. Electrons generated by the oxidation of CO at the C and C’ clusters are transferred to the internal redox chain in CODH, consisting of B (and B’) and D FeS clusters. The D-cluster, located at the interface between the two subunits, is proposed to transfer electrons to the electron transfer protein (Coof), which is coupled to hydrogenase. (From Ragsdale & Pierce, Copyright 2008 with permission from Elsevier.)
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FIGURE 15.5 The C-cluster of CODH and the A-cluster of ACS. (From Ragsdale, Copyright 2007 with permission from Elsevier.)
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FIGURE 15.6 Structure of P430 at the MCR active site and mechanism of methane formation. The structure was derived from PDB code 1HBN. The bound CoM was omitted from the structure to focus on the tetrapyrrole. (From Ragsdale, Copyright 2009 with permission from Elsevier.)
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FIGURE 15.7 Ball and stick representation of adenosylcobalamin. (From Reed, Copyright 2004 with permission from Elsevier.)
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FIGURE 15.8 Structures of cobalamin derivatives and the various ligation states. (From Banerjee, Gherasim, & Padovani, Copyright 2009 with permission from Elsevier.)
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FIGURE 15.9 General reaction mechanism for AdoCbl-dependent isomerases. (From Banerjee & Ragsdale, Reprinted with permission from Annual Reviews.)
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FIGURE (a) The three components involved in the B12-dependent methyltransferases. (b) The MT2 enzymes have a thiol group which activates the thiol acceptor. (From Banerjee & Ragsdale, Reprinted with permission from Annual Reviews.)
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FIGURE Reactions catalysed by cobalamin-dependent methionine synthase. (From Banerjee & Ragsdale, Reprinted with permission from Annual Reviews.)
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FIGURE The modular structure of methionine synthase. The four domains are connected by flexible hinges which allow the CH3tetrahydrofolate-, AdoMet-, or homocystein-binding domains to alternatively access the B12-binding domain. (From Banerjee & Ragsdale, Reprinted with permission from Annual Reviews.)
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FIGURE Type 1 and type 2 MetAPs (“pita-bread” enzymes). (a) E. coli MetAP-1; (b) P. furiosis MetAP-2; (c) human MetAP-2. In contrast to the type 1 enzymes, type 2 MetAPs contain an -helical subdomain (orange) inserted within the catalytic domain (cyan and green -helices and -strands, respectively). (From Lowther & Matthews, Reprinted with permission of the American Chemical Society.)
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FIGURE Comparison of the dinuclear metal centres and flanking His residues of E. coli MetAP-1 (red) and its relatives. (From Lowther & Matthews, Reprinted with permission of the American Chemical Society.)
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Table 15.1
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UnnFIGURE 15.1
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