1ppp
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(New page: 200px<br /><applet load="1ppp" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ppp, resolution 1.9Å" /> '''CRYSTAL STRUCTURE OF ...)
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CRYSTAL STRUCTURE OF PAPAIN-E64-C COMPLEX. BINDING DIVERSITY OF E64-C TO PAPAIN S2 AND S3 SUBSITES
Overview
In order to investigate the binding mode of E64-c (a synthetic cysteine, proteinase inhibitor) to papain at the atomic level, the crystal structure, of the complex was analysed by X-ray diffraction at 1.9 A (1 A is, expressed in SI units as 0.1 nm) resolution. The crystal has a space group, P2(1)2(1)2(1) with a = 43.37, b = 102.34 and c = 49.95 A. A total of, 21,135 observed reflections were collected from the same crystal, and, 14811 unique reflections of up to 1.9 A resolution [Fo > 3 sigma(Fo)] were, used for the structure solution and refinement. The papain structure was, determined by means of the molecular replacement method, and then the, inhibitor was observed on a (2 magnitude of Fo-magnitude of Fc) difference, Fourier map. The complex structure was finally refined to R = 19.4%, including 207 solvent molecules. Although this complex crystal (Form II), was polymorphous as compared with the previously analysed one (Form I), the binding modes of leucine and isoamylamide moieties of E64-c were, significantly different from each other. By the calculation of accessible, surface area for each complex atom, these two different binding modes were, both shown to be tight enough to prevent the access of solvent molecules, to the papain active site. With respect to the E64-c-papain binding mode, molecular-dynamics simulations proposed two kinds of stationary states, which were derived from the crystal structures of Forms I and II. One of, these, which corresponds to the binding mode simulated from Form I, was, essentially the same as that observed in the crystal structure, and the, other was somewhat different from the crystal structure of Form II, especially with respect to the binding of the isoamylamide moiety with the, papain S subsites. The substrate specificity for the papain active site is, discussed on the basis of the present results.
About this Structure
1PPP is a Single protein structure of sequence from [1] with E6C and MOH as ligands. Active as Lyase, with EC number 4.3.22.2 Full crystallographic information is available from OCA.
Reference
Crystal structure of papain-E64-c complex. Binding diversity of E64-c to papain S2 and S3 subsites., Kim MJ, Yamamoto D, Matsumoto K, Inoue M, Ishida T, Mizuno H, Sumiya S, Kitamura K, Biochem J. 1992 Nov 1;287 ( Pt 3):797-803. PMID:1445241
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