Examine the following proteins and determine how many domains each polypeptide h

Question

Examine the following proteins and determine how many domains each polypeptide has. (If there is more than one chain or model, only examine one.) List the residues in each domain (e.g. 17-98, 141-169), and classify each domain (as in part 1).

1. One subunit of human branched chain aminotransferase (4HBA)

2. Escherichia carbenicillin-binding protein (5ECB)

3. One subunit of the enterobacterial ligand-gated ion channel (6ELC)

C. Examine the following multimeric proteins and classify the symmetrical arrangement of the subunits (e.g. C2, C3, D2, helical, icosahedral). If the program asks you to “Load __ models”, just hit OK with whatever number it has by default. (Note that each model will load as a different layer.)

1. Nitrosomonas hydroxylamine oxidoreductase (7NHO)

2. Enterobacterial lectin (8EBL)

3. Enterobacterial ligand-gated ion channel (6ELC)

D. Examine the 2 pairs of proteins below. In each case, these are enzymes that catalyze the same reaction in different species. The question is: are they related or not? i.e. Are the structures essentially the same? Often you can get similar reactions from proteins that evolved from a common ancestor (e.g. trypsin and chymotrypsin). Sometimes the same reaction can be catalyzed by proteins with very different evolutionary origins and with very different structures (e.g. trypsin and subtilisin). Your job is to decide if these proteins have fundamentally different folds or if they have basically the same fold. Briefly justify your answer (3 sentences).

Aldolase from an Archaea and a Bacillus (PR1A & PR1B)

Isochorismate synthase from a Proteobacterium and a Bacillus (PR2A & PR2B)

Explanation / Answer

Hi,

as per our regulations, first full question is answered.

B. Proten domain analysis: these can be solved by looking for protein name in uniprot or in pfam . these have details about the protein domain, sequences, structures...etc.

1. One subunit of human branched chain aminotransferase (4HBA):

domain : 1

type: Amino-transferase class IV

amino acids: 107 - 360

CBP

domain: 3

domain ;amino acid range

MecA_N ;25- 140

PBP_dimer ;146- 314

Transpeptidase ;347- 660

lingand gated ion channel

domain: 2

neu chan LBD ; 33-177

neu chan membrane: 237 - 336

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