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The structure of a metalloenzyme active site is down below(black picture). Describe, from a chemical and structural perspective, how the reactive site is designed to facilitate its catalytic reaction. The example below(white pitcure) suggests the level of detail that is required. Make sure that you explain what the metal is doing, what the reaction is, and its biological significance.

The structure of a metalloenzyme active site is down below(black picture). Describe, from a chemical and structural perspective, how the reactive site is designed to facilitate its catalytic reaction. The example below(white pitcure) suggests the level of detail that is required. Make sure that you explain what the metal is doing, what the reaction is, and its biological significance.

Biochemistry
Biochemistry
9th Edition
ISBN:9781319114671
Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.
Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.
Chapter1: Biochemistry: An Evolving Science
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The structure of a metalloenzyme active site is down below(black picture). Describe, from a chemical and structural perspective, how the reactive site is designed to facilitate its catalytic reaction. The example below(white pitcure) suggests the level of detail that is required. Make sure that you explain what the metal is doing, what the reaction is, and its biological significance.  

 

 

A CH MMOB MMOH W308-Tunnel Diiron cluster PDB:6YDI This is the structure of the active site of soluble methane monooxygenase, an enzyme that catalyzes the redox reaction that transforms CH4 and O₂ to CH3OH and H₂O. This reaction allows methanotrophic organisms to use methanol as fuel. The redox is accomplished at a diiron cluster, which, in the ferrous (+2) state, is able to reduce O₂ to form a highly oxidized diiron(IV) (+4) species termed Q. Q is a strong oxidizing agent able generate methanol by oxidizing methane. The diiron cluster has no inherent specificity that would allow is to react only with CH4 and O₂ but the enzyme structure around the cluster shown here helps to explain the selectivity of the enzyme. There is a channel shown in blue lined with hydrophobic amino acids leading to the active diiron. The hydrophobic nature facilitates passage of non-polar molecules like CH4 and O₂. Structural changes in the MMOB and MMOH proteins during the reaction cycle constrict the channel at the dashed box so that only O₂ can pass through when the diiron is in the reducing +2 state and methane when it is in the +4 state. This selectivity is key for the organism to effectively use methane as fuel.
Transcribed Image Text:A CH MMOB MMOH W308-Tunnel Diiron cluster PDB:6YDI This is the structure of the active site of soluble methane monooxygenase, an enzyme that catalyzes the redox reaction that transforms CH4 and O₂ to CH3OH and H₂O. This reaction allows methanotrophic organisms to use methanol as fuel. The redox is accomplished at a diiron cluster, which, in the ferrous (+2) state, is able to reduce O₂ to form a highly oxidized diiron(IV) (+4) species termed Q. Q is a strong oxidizing agent able generate methanol by oxidizing methane. The diiron cluster has no inherent specificity that would allow is to react only with CH4 and O₂ but the enzyme structure around the cluster shown here helps to explain the selectivity of the enzyme. There is a channel shown in blue lined with hydrophobic amino acids leading to the active diiron. The hydrophobic nature facilitates passage of non-polar molecules like CH4 and O₂. Structural changes in the MMOB and MMOH proteins during the reaction cycle constrict the channel at the dashed box so that only O₂ can pass through when the diiron is in the reducing +2 state and methane when it is in the +4 state. This selectivity is key for the organism to effectively use methane as fuel.
A B 172 spmoB 265 spmoBd2 spmoBd1 See this image and copyright information in PMC Figure 1 Overall architecture of pMMO. (A) Structure of Methylocystis sp. strain M pMMO protomer (PDB accession code 3RGR). The pmoB, pmoA, and pmoC subunits are shown in blue, magenta, and green, respectively. The N- and C-termini of pmoB are labeled. An exogenous helix is shown in yellow. Copper ions are shown as cyan spheres and a zinc ion is shown as a gray sphere. Ligands are shown as ball-and-stick representations. (B) Structure of M. capsulatus (Bath) pMMO protomer (PDB accession code 3RGB). The amino terminal domain of pmoB (spmoBd1) is shown in blue, the carboxy terminal domain of pmoB is shown in gray (spmoBd2), and the two transmembrane helices are shown in transparent blue. In the recombinant spmoB protein, spmoBd1 and spmoBd2 are linked by a GKLGGG sequence connecting residues 172 and 265 (labeled). The pmoA and pmoC subunits are shown in transparent magenta and transparent green, respectively. A hydrophilic patch of residues proposed to house a tricopper active site is denoted with an asterisk. The mononuclear copper site at the interface of the two spmoB domains is not present in the Methylocystis sp. strain M pMMO structure. [A color version of this figure is available online.]
Transcribed Image Text:A B 172 spmoB 265 spmoBd2 spmoBd1 See this image and copyright information in PMC Figure 1 Overall architecture of pMMO. (A) Structure of Methylocystis sp. strain M pMMO protomer (PDB accession code 3RGR). The pmoB, pmoA, and pmoC subunits are shown in blue, magenta, and green, respectively. The N- and C-termini of pmoB are labeled. An exogenous helix is shown in yellow. Copper ions are shown as cyan spheres and a zinc ion is shown as a gray sphere. Ligands are shown as ball-and-stick representations. (B) Structure of M. capsulatus (Bath) pMMO protomer (PDB accession code 3RGB). The amino terminal domain of pmoB (spmoBd1) is shown in blue, the carboxy terminal domain of pmoB is shown in gray (spmoBd2), and the two transmembrane helices are shown in transparent blue. In the recombinant spmoB protein, spmoBd1 and spmoBd2 are linked by a GKLGGG sequence connecting residues 172 and 265 (labeled). The pmoA and pmoC subunits are shown in transparent magenta and transparent green, respectively. A hydrophilic patch of residues proposed to house a tricopper active site is denoted with an asterisk. The mononuclear copper site at the interface of the two spmoB domains is not present in the Methylocystis sp. strain M pMMO structure. [A color version of this figure is available online.]
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