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High-resolution structure of the complex between carboxypeptidase A and L-phenyl lactate.

Teplyakov A, Wilson KS, Orioli P, Mangani S
Acta Crystallogr D Biol Crystallogr 49 534-40 (1993)
Cited: 24 times
EuropePMC logo PMID: 15299490

Abstract

The X-ray structures of native carboxypeptidase A and of the enzyme-inhibitor complex with L-phenyl lactate have been refined at 1.54 and 1.45 A resolution to R factors of 0.151 and 0.161, respectively. Crystals of the complex were isomorphous with the native crystals (space group P2(1), a = 51.60, b = 60.27, c = 47.25 A, beta = 97.27 degrees ). The high-resolution electron density allowed correction of many side-chain positions in the classical carboxypeptidase A model. This reflects the advantages of the high-quality complete synchrotron data collected with an imaging plate detector. The conformational changes in the active centre of the enzyme upon binding of the inhibitor are restricted to only two residues, Tyr248 and Arg145. L-Phenyl lactate is bound in the S1' pocket and forms hydrogen bonds to Arg145, Glu270 and to the zinc-bound water molecule. The present structure provides an explanation for the higher stability of the complexes with the products of esterolysis in comparison with those of amidolysis. This is consistent with the finding that product release is rate limiting for esters but not for peptides.

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  3. Reconstruction of ancestral protein sequences and its applications. Cai W, Pei J, Grishin NV. BMC Evol. Biol. 4 33 (2004)
  4. Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics. Azuara C, Orland H, Bon M, Koehl P, Delarue M. Biophys. J. 95 5587-5605 (2008)
  5. Beyond the Poisson-Boltzmann model: modeling biomolecule-water and water-water interactions. Koehl P, Orland H, Delarue M. Phys. Rev. Lett. 102 087801 (2009)
  6. Binding cavities and druggability of intrinsically disordered proteins. Zhang Y, Cao H, Liu Z. Protein Sci 24 688-705 (2015)
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  8. Improving the performance of the PLB index for ligand-binding site prediction using dihedral angles and the solvent-accessible surface area. Cao C, Xu S. Sci Rep 6 33232 (2016)
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  10. A convenient protein library for spectroscopic calibrations. De Meutter J, Goormaghtigh E. Comput Struct Biotechnol J 18 1864-1876 (2020)
  11. A new definition and properties of the similarity value between two protein structures. Saberi Fathi SM. J Biol Phys 42 621-636 (2016)


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  1. Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs. Böhm HJ. J. Comput. Aided Mol. Des. 12 309-323 (1998)
  2. Progress in metallocarboxypeptidases and their small molecular weight inhibitors. Fernández D, Pallarès I, Vendrell J, Avilés FX. Biochimie 92 1484-1500 (2010)

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  2. Consensus scoring for ligand/protein interactions. Clark RD, Strizhev A, Leonard JM, Blake JF, Matthew JB. J. Mol. Graph. Model. 20 281-295 (2002)
  3. Packing at the protein-water interface. Gerstein M, Chothia C. Proc. Natl. Acad. Sci. U.S.A. 93 10167-10172 (1996)
  4. X-ray structure of pyrrolidone carboxyl peptidase from the hyperthermophilic archaeon Thermococcus litoralis. Singleton M, Isupov M, Littlechild J. Structure 7 237-244 (1999)
  5. New approach for local structure analysis of the tyrosine domain in proteins by using a site-specific and polarity-sensitive fluorescent probe. Chen S, Li X, Ma H. Chembiochem 10 1200-1207 (2009)
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  10. Comparison of Composer and ORCHESTRAR. Dolan MA, Keil M, Baker DS. Proteins 72 1243-1258 (2008)
  11. Zn2+-dependent autocatalytic activity of the Bordetella pertussis CyaA-hemolysin. Raksanoh V, Shank L, Prangkio P, Yentongchai M, Sakdee S, Imtong C, Angsuthanasombat C. Biochem. Biophys. Res. Commun. 485 720-724 (2017)


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