BIOCHEM. http://www.rcsb.org/pad/home/home.do 7. Protein structure. Examine the

Question

BIOCHEM. http://www.rcsb.org/pad/home/home.do 7. Protein structure. Examine the three-dimensional atomic structure of the protein EF-G-2 from the bacterium Thermus thermophilus. Find the atomic coordinates of the crystal structure of this protein at http://www.rcsb.org/pdb/home/home.do . Look for the file name called 2DY1. Visualize the structure using Jmol software (http://bioinformatics.org firstglancefg ). Answer the following questions. A) How many amino acid residues are in EF-G-2 B) What is the resolution of the crystal structure? C) What ligand is bound to EF-G-2? D) Describe the topology of domain 3 of EF-G-2. How many -helices and -strands? Are the -strands parallel or anti-parallel? What neighboring domains interact non-covalently with domain 3? Find the amino acid residue Glu187. This residue makes electrostatic interactions with residue Find Lys469. In what type of secondary structure is this residue? This residue makes hydrogen bonds with residue E) F) G) which residues are part of -turns? [Circle the numbers corresponding to these residues.] 415 417 419 421 H) Which residues are part of the hydrophobic core of EF-G-2? [Circle the numbers corresponding to these residues.] 402 403 406 407

Explanation / Answer

a)

1-658 amino acids residues are there

b)

crystal resolution through x ray diffraction is 1.6 Armstrong

C)

two ligands bound to EF-G-2

1--> MG 701 (A)

2--> GTP 700 (A)

d)

EF -G- 2 is folded into 5 domains with

Domain 1 and 2 forming N terminal block and domain 4 and 5 forming C terminal block

Domain 3 provides the covalent link flexible connection btweeen the two. 2 beta sheets are Present.....beta sheets are antiparallel to each other.

E)

Glu 187 makes ionic interaction with Glu 188.

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