PDBsum entry 1rd2

Ribonucleic acid

PDB id: 1rd2

Contents

DNA/RNA

Theoretical model

PDB id:

1rd2

Name:

Ribonucleic acid

Title:

The interaction between mRNA and tRNA (model d2)

Structure:

P-site tRNA. Chain: a. Engineered: yes. A-site tRNA. Chain: b. Engineered: yes. Single-stranded mRNA. Chain: c. Engineered: yes

Source:

Synthetic: yes. Synthetic: yes

Authors:

C.Liu,X.Wang

Key ref:

R.L.Walter et al. (1996). Multiple wavelength anomalous diffraction (MAD) crystal structure of rusticyanin: a highly oxidizing cupredoxin with extreme acid stability. J Mol Biol, 263, 730-751. PubMed id: 8947572 DOI: 10.1006/jmbi.1996.0612

Date:

05-Nov-03 Release date: 18-Nov-03

DNA/RNA chains

G-C-G-G-A-U-U-U-A-2MG-C-U-C-A-G-H2U-H2U-G-G-G-A-G-A-G-C-M2G-C-C-A-G-A-OMC-U ... 76 bases

G-C-G-G-A-U-U-U-A-2MG-C-U-C-A-G-H2U-H2U-G-G-G-A-G-A-G-C-M2G-C-C-A-G-A-OMC-U ... 76 bases

G-G-C-G-G-U-U-G-C-A-G-G-U-C-U-G-C-A-C-C-G-C-C 23 bases

DOI no: 10.1006/jmbi.1996.0612

J Mol Biol 263:730-751 (1996)

PubMed id: 8947572

Multiple wavelength anomalous diffraction (MAD) crystal structure of rusticyanin: a highly oxidizing cupredoxin with extreme acid stability.

R.L.Walter, S.E.Ealick, A.M.Friedman, R.C.Blake, P.Proctor, M.Shoham.

ABSTRACT

The X-ray crystal structure of the oxidized form of the extremely stable and highly oxidizing cupredoxin rusticyanin from Thiobacillus ferrooxidans has been determined by the method of multiwavelength anomalous diffraction (MAD) and refined to 1.9 A resolution. Like other cupredoxins, rusticyanin is a copper-containing metalloprotein, which is composed of a core beta-sandwich fold. In rusticyanin the beta-sandwich is composed of a six- and a seven-stranded beta-sheet. Also like other cupredoxins, the copper ion is coordinated by a cluster of four conserved residues (His85, Cys138, His143, Met148) arranged in a distorted tetrahedron. Rusticyanin has a redox potential of 680 mV, roughly twice that of any other cupredoxin, and it is optimally active at pH values < or = 2. By comparison with other cupredoxins, the three-dimensional structure of rusticyanin reveals several possible sources of the chemical differences, including more ordered secondary structure and more intersheet connectivity than other cupredoxins. The acid stability and redox potential of rusticyanin may also be enhanced over other cupredoxins by a more extensive internal hydrogen bonding network and by more extensive hydrophobic interactions surrounding the copper binding site. Finally, reduction in the number of charged residues surrounding the active site may also make a major contribution to acid stability. We propose that the resulting rigid copper binding site, which is constrained by the surrounding hydrophobic environment, structurally and electronically favours Cu(I). We propose that the two extreme chemical properties of rusticyanin are interrelated; the same unique structural features that enhance acid stability also lead to elevated redox potential.

Selected figure(s)

Figure 3.
Figure 3. The b-bulge connection between sheets one and two in rusticyanin. The indole ring of Trp7 from strand one inserts into the bulge formed by Gly110, Phe111, Ser112, and Pro113 from strand 10. It is anchored by both polar and hydrophobic interactions. The Figure was prepared using MOLSCRIPT (Kraulis, 1991).

Figure 8.
Figure 8. Stereoview of the hydrogen bonding network surrounding the partially buried residue Asp88. This network provides stability between strands 9, 10 and 12 as well as helping to fix the orientation of the side-chain of Cys138. The fourth copper ligand, Met148, has been omitted from this Figure for the sake of clarity.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 263, 730-751) copyright 1996.

Figures were selected by an automated process.