Bioformatics Homework 3

1. Trp repressor

(i) Trp repressor itself

1. ID number : 1WRP
2. Authors : R. W. Schewitz, Z. Otwinowski, C. L. Lawson, A. J. Joachimiak, P. B. Sigler
3. Resolution : 2.2 Angstroms
4. 108 residues in one monomer

script

	select all

	wireframe off

	cartoon on

	color chain

	select 77

	spacefill on

	color yellow

(ii) Trp repressor complexed with its operator

1. ID number : 1TRO
2. Authors : Z. Otwinowski, R. G. Zhang, P. B. Sigler
3. Resolution : 1.9 Angstroms
4. 108 residues in one monomer
5. 2 cofactors in whole complex (dimeric protein, one cofactor per monomer)

script

	select all

	cartoon on

	wireframe off

	select *a

	color cyan

	select *c

	color greenblue

	select *e

	color orange

	select *g

	color red

	select *i

	color violet

	select *j

	color green

	select *k

	color magenta

	select *l

	color redorange

	select *b,*d,*f,*h

	spacefill on

	color blue

	select 77

	spacefill on

	color yellow

Mechanism

In the presence of excess tryptophan, trp repressor binds tryptophan, and the repressor-tryptophan complex binds to the operator trpO, which lies within the promoter.When bound to trpO, the repressor-tryptophan complex prevents RNA polymerase from binding to the promoter.

2. Arc repressor

DNA sequences of the Arc repressor

the distance between possible hydrogen bonds