Analysis of a new crystal form of procarboxypeptidase B: further insights into the catalytic mechanism.

Abstract:

:A new triclinic crystal structure form of porcine pancreatic procarboxypeptidase B (PCPB) was obtained at higher resolution than the previously known tetragonal crystal structure. This new crystal polymorph has allowed for a corrected, accurate assignment of residues along the polypeptide chain based on the currently available gene sequence information and crystallographic data. The present structure shows unbound PCPB in a distinct molecular packing as compared to the previous benzamidine complexed form. Its catalytically important Tyr248 residue is oriented and hydrogen-bonded to solvent water molecules, and locates the furthest away from the catalytic zinc ion as compared to previous structures. A relatively long stretch of residues flanking Tyr248 and guarding the access to the catalytic zinc ion was found to be sequentially unique to the M14 family of peptidases. Predictions from a normal mode analysis indicated that this stretch of residues belongs to a rigid subdomain in the protein structure. The specific presence of a tyrosyl residue at the most exposed position in this region would allow for a delicate balance between extreme hydrophobicity and hydrophilicity, and affect substrate binding and the kinetic efficiency of the enzyme.

journal_name

Biopolymers

journal_title

Biopolymers

authors

Fernández D,Boix E,Pallarès I,Avilés FX,Vendrell J

doi

10.1002/bip.21320

subject

Has Abstract

pub_date

2010-02-01 00:00:00

pages

178-85

issue

2

eissn

0006-3525

issn

1097-0282

journal_volume

93

pub_type

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