PDBsum entry 1prv

DNA binding protein

PDB id: 1prv

Contents

Protein chain

56 a.a. *

* Residue conservation analysis

PDB id:

1prv

Name:

DNA binding protein

Title:

Purine repressor DNA-binding domain DNA binding

Structure:

Purine repressor. Chain: a. Fragment: DNA-binding. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

NMR struc:

20 models

Authors:

A.Nagadoi,S.Morikawa,H.Nakamura,M.Enari,K.Kobayashi,H.Yamamoto, G.Sampei,K.Mizobuchi,M.A.Schumacher,R.G.Brennan,Y.Nishimura

Key ref:

A.Nagadoi et al. (1995). Structural comparison of the free and DNA-bound forms of the purine repressor DNA-binding domain. Structure, 3, 1217-1224. PubMed id: 8591032 DOI: 10.1016/S0969-2126(01)00257-X

Date:

08-May-95 Release date: 08-Mar-96

Protein chain

P0ACP7  (PURR_ECOLI) -  HTH-type transcriptional repressor PurR from Escherichia coli (strain K12)

Seq: 341 a.a.

Struc: 56 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/S0969-2126(01)00257-X

Structure 3:1217-1224 (1995)

PubMed id: 8591032

Structural comparison of the free and DNA-bound forms of the purine repressor DNA-binding domain.

A.Nagadoi, S.Morikawa, H.Nakamura, M.Enari, K.Kobayashi, H.Yamamoto, G.Sampei, K.Mizobuchi, M.A.Schumacher, R.G.Brennan.

ABSTRACT

BACKGROUND: The purine repressor (PurR) regulates genes that encode enzymes for purine biosynthesis. PurR has a two domain structure with an N-terminal DNA-binding domain (DBD) and a C-terminal corepressor-binding domain (CBD). The three dimensional structure of a ternary complex of PurR bound to both corepressor and a specific DNA sequence has recently been determined by X-ray crystallography. RESULTS: We have determined the solution structure of the PurR DBD by NMR. It contains three helices, with the first and second helices forming a helix-turn-helix motif. The tertiary structure of the three helices is very similar to that of the corresponding region in the ternary complex. The structure of the hinge helical region, however, which makes specific base contacts in the minor groove of DNA, is disordered in the DNA-free form. CONCLUSION: The stable formation of PurR hinge helices requires PurR dimerization, which brings the hinge regions proximal to each other. The dimerization of the hinge helices is likely to be controlled by the CBD dimerization interface, but is induced by specific-DNA binding.

Selected figure(s)

Figure 3.
Figure 3. Stereoview of the best-fit superpositions of the 20 PurN56 structures, along with the refined average structure. Met1–Pro47 is shown in yellow for the 20 structures and in red for the average structure, and Ser48–Val56 is green for the 20 structures. No average structure is shown for the C-terminal residues. Figure 3. Stereoview of the best-fit superpositions of the 20 PurN56 structures, along with the refined average structure. Met1–Pro47 is shown in yellow for the 20 structures and in red for the average structure, and Ser48–Val56 is green for the 20 structures. No average structure is shown for the C-terminal residues.

Figure 7.
Figure 7. A best-fit superposition of the free PurR DBD structure onto the ternary complex structure of the PurR–hypoxanthine–purF-operator. The backbone atoms of the free PurR DBD (Met1–Ser48) are shown in yellow, and the backbone atoms of PurR dimer in the ternary complex are shown in blue and red, the two colours distinguishing the two monomers. The DNA atoms are shown in pink and white. Two hypoxanthine molecules bound to PurR dimer are also shown in white. Figure 7. A best-fit superposition of the free PurR DBD structure onto the ternary complex structure of the PurR–hypoxanthine–purF-operator. The backbone atoms of the free PurR DBD (Met1–Ser48) are shown in yellow, and the backbone atoms of PurR dimer in the ternary complex are shown in blue and red, the two colours distinguishing the two monomers. The DNA atoms are shown in pink and white. Two hypoxanthine molecules bound to PurR dimer are also shown in white.

The above figures are reprinted by permission from Cell Press: Structure (1995, 3, 1217-1224) copyright 1995.

Figures were selected by an automated process.