3sc2
From Proteopedia
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REFINED ATOMIC MODEL OF WHEAT SERINE CARBOXYPEPTIDASE II AT 2.2-ANGSTROMS RESOLUTION
Overview
The crystal structure of the homodimeric serine carboxypeptidase II from, wheat (CPDW-II, M(r) 120K) has been determined and fully refined at 2.2-A, resolution to a standard crystallographic R factor of 16.9% using, synchrotron data collected at the Brookhaven National Laboratory. The, model has an rms deviation from ideal bond lengths of 0.018 A and from, bond angles of 2.8 degrees. The model supports the general conclusions of, an earlier study at 3.5-A resolution and will form the basis for, investigation into substrate binding and mechanistic studies. The enzyme, has an alpha + beta fold, consisting of a central 11-stranded beta-sheet, with a total of 15 helices on either side. The enzyme, like other serine, proteinases, contains a "catalytic triad" Ser146-His397-Asp338 and a, presumed "oxyanion hole" consisting of the backbone amides of Tyr147 and, Gly53. The carboxylate of Asp338 and imidazole of His397 are not coplanar, in contrast to the other serine proteinases. A comparison of the active, site features of the three families of serine proteinases suggests that, the "catalytic triad" should actually be regarded as two diads, a His-Asp, diad and a His-Ser diad, and that the relative orientation of one diad, with respect to the other is not particularly important. Four active site, residues (52, 53, 65, and 146) have unfavorable backbone conformations but, have well-defined electron density, suggesting that there is some strain, in the active site region. The binding of the free amino acid arginine has, been analyzed by difference Fourier methods, locating the binding site for, the C-terminal carboxylate of the leaving group. The carboxylate makes, hydrogen bonds to Glu145, Asn51, and the amide of Gly52. The carboxylate, of Glu145 also makes a hydrogen bond with that of Glu65, suggesting that, one or both may be protonated. Thus, the loss of peptidase activity at pH, > 7 may in part be due to deprotonation of Glu145. The active site does, not reveal exposed peptide amides and carbonyl oxygen atoms that could, interact with substrate in an extended beta-sheet fashion. The fold of the, polypeptide backbone is completely different than that of trypsin or, subtilisin, suggesting that this is a third example of convergent, molecular evolution to a common enzymatic activity. Furthermore, it is, suggested that the active site sequence motif "G-X-S-X-G/A", often, considered the hallmark of serine peptidase or esterase activity, is, fortuitous and not the result of divergent evolution.(ABSTRACT TRUNCATED, AT 400 WORDS)
About this Structure
3SC2 is a Single protein structure of sequence from [1]. This structure superseeds the now removed PDB entry 2SC2. Active as Hydrolase, with EC number and 3.4.16.6 3.4.16.5 and 3.4.16.6 Full crystallographic information is available from OCA.
Reference
Refined atomic model of wheat serine carboxypeptidase II at 2.2-A resolution., Liao DI, Breddam K, Sweet RM, Bullock T, Remington SJ, Biochemistry. 1992 Oct 13;31(40):9796-812. PMID:1390755
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