2. Transcription of the ant gene during lytic growth of bacteriophage P22 is regulated by the cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Please find the co-crystal structure of this Arc tetramer-operator complex from PDB.
(a) Make an animation (by Gifbuilder) of whole complex.
(b) Show the DNA sequences of the Arc operator.
(c) The picture below is the hydrogen bonds between beta-sheet side chains and DNA bases. Show three side chains (gln9, asn11, arg13) from one monomer and corresponding DNA bases of them on your home page. Color three side chain with different color. Measure the distance between possible hydrogen bonds.
1.Ans :
(1) ID numbers : 1TRO
(2) Authors : Z.OTWINOWSKI, R. G. ZHANG, P. B. SIGLER
(3) Resolution : 1.9 ANGSTRONS
(4) How many residues in one monomer : 108
(5) How may cofactors in whole complex : 4
Trp repressor complex :
Script :
select all wireframe off select *a,*c,*e,*g,*i,*j,*k,*l cartoon select *a color [255,170,170] select *c color [255,90,90] select *e color [90,90,255] select*g color [180,180,255] select *i color [255,255,140] select *j color [255,180,100] select *k color [170,255,170] select *l color [90,255,190] select *b,*d,*f,*h color [0,0,255] set ambient 35
2.Ans :
Arc Repressor Complex :
DNA Sequence of the Arc
Repressor :
| 5' | T | A | T | A | G | T | A | G | A | G | T | G | C | T | T | C | T | A | T | C | A | T | 3' | |||
| 3' | T | A | T | C | A | T | C | T | C | A | C | G | A | A | G | A | T | A | G | T | A | A | 5' |
Gln9A,Asn11A and Arg13A
Gln9 A -- A18F : 3.316A
Asn11A -- A7 E : 3.239A
Arg13A -- G8 E : 2.669A
Gln9 B -- A7 E : 2.803A
Asn11B -- T17F : 3.374A
Arg13B -- G5 E : 3.629A
Asn11A -- A7 E : 3.239A
Arg13A -- G8 E : 2.669A
Gln9 B -- A7 E : 2.803A
Asn11B -- T17F : 3.374A
Arg13B -- G5 E : 3.629A