Go to www.pdb.org and examine the pdb file 1 L.M 1 for glutamate synthase. Find its iron-sulfur cluster and FMN prosthetic group. Discover how this enzyme is organized into an N-terminal domain that functions in ammonia removal from glutamine (the glutaminase domain ) and the \(\alpha\) -ketoglutarate-binding site near the \(\mathrm{Fe} / \mathrm{S}\) and flavin prosthetic groups. Consult van den Heuvel, R. H. H., et al., \(2002 .\) Structural studies on the synchronization of catalytic centers in glutamate synthase. Journal of Biological Chemistry 277: \(24579-24583,\) to see how these two sites are connected by a tunnel for passage of ammonia from glutamine to \(\alpha\) -ketoglutarate.

Step by step solution

01

Access and examine the pdb file

Go to www.pdb.org. In the search bar, enter the pdb file number 1 L.M 1, and press enter. A three-dimensional structure of the enzyme glutamate synthase should appear.

02

Identify the iron-sulfur cluster and FMN prosthetic group

In the protein structure, locate and examine the iron-sulfur cluster and the FMN prosthetic group. These structural components are crucial for understanding the enzyme function.

03

Discover enzyme organization

Look for the N-terminal domain of the enzyme, which is responsible for ammonia removal from glutamine (the glutaminase domain) and the alpha-ketoglutarate-binding site located near the iron/sulfur and flavin prosthetic groups.

04

Consult study and observe tunnel

Consult the study from van den Heuvel, R. H. H., et al., 2002, titled 'Structural studies on the synchronization of catalytic centers in glutamate synthase'. In this study, notice the connection of two sites by a tunnel that allows for the passage of ammonia from glutamine to alpha-ketoglutarate.

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