PDBsum entry 4z65

Hydrolase

PDB id: 4z65

Contents

Protein chain

304 a.a.

Ligands

0X9

Metals

_ZN ×2

Waters ×329

PDB id:

4z65

Name:

Hydrolase

Title:

Carboxypeptidase b with sulphamoil arginine

Structure:

Carboxypeptidase b. Chain: a. Fragment: unp residues 113-416. Engineered: yes

Source:

Sus scrofa. Pig. Organism_taxid: 9823. Gene: cpb1, cpb. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.25Å R-factor: 0.160 R-free: 0.180

Authors:

V.I.Timofeev,V.K.Akparov,I.P.Kuranova

Key ref:

V.Akparov et al. (2015). Structure of the complex of carboxypeptidase B and N-sulfamoyl-L-arginine. Acta Crystallogr F Struct Biol Commun, 71, 1335-1340. PubMed id: 26457527 DOI: 10.1107/S2053230X15016799

Date:

03-Apr-15 Release date: 14-Oct-15

Protein chain

P09955  (CBPB1_PIG) -  Carboxypeptidase B from Sus scrofa

Seq: 416 a.a.

Struc: 304 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.17.2 - carboxypeptidase B.
• Reaction: Peptidyl-L-lysine(or L-arginine) + H(2)O = peptide + L-lysine(or L- arginine)
• Cofactor: Zn(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1107/S2053230X15016799

Acta Crystallogr F Struct Biol Commun 71:1335-1340 (2015)

PubMed id: 26457527

Structure of the complex of carboxypeptidase B and N-sulfamoyl-L-arginine.

V.Akparov, N.Sokolenko, V.Timofeev, I.Kuranova.

ABSTRACT

Porcine pancreatic carboxypeptidase B (EC 3.4.23.6) was complexed with a stable transition-state analogue, N-sulfamoyl-L-arginine, in which an S atom imitates the sp(3)-hybridized carbon in the scissile-bond surrogate. Crystals were grown in a form belonging to the same space group, P41212, as the uncomplexed enzyme. X-ray data were collected to a resolution of 1.25 Å. The molecule was refined and the positions of non-H atoms of the inhibitor and water molecules were defined using difference Fourier maps. The enzyme-inhibitor complex and 329 water molecules were further refined to a crystallographic R factor of 0.159. The differences in conformation between the complexed and uncomplexed forms of carboxypeptidase B are shown. The inhibitor is bound in a curved conformation in the active-site cleft, and the sulfamide group is bound to the Zn ion in an asymmetric bidentate fashion. The complex is stabilized by hydrogen bonds between the N1/N2 guanidine group of the inhibitor and the Asp255 carboxyl of the enzyme. The side-chain CH2 groups of the inhibitor are in van der Waals contact with Leu203 and Ile247 in the enzyme. This study provides useful clues concerning how the transition state of arginine may bind to carboxypeptidase B and therefore provides an insight into the structural basis of carboxypeptidase B selectivity, which is useful for the rational design of a carboxypeptidase with improved selectivity for industrial recombinant pro-insulin processing.