PDBsum entry 1p05

Hydrolase/hydrolase inhibitor

PDB id: 1p05

Contents

Protein chain

198 a.a. *

Ligands

ALA-ALA-PRO-BNO

SO4

Waters ×174

* Residue conservation analysis

PDB id:

1p05

Name:

Hydrolase/hydrolase inhibitor

Title:

Structure analysis of specificity. Alpha-lytic protease complexes with analogues of reaction intermediates

Structure:

Alpha-lytic protease. Chain: a. Engineered: yes. Methoxysuccinyl-ala-ala-pro-norleucine boronic acid inhibitor. Chain: p. Engineered: yes

Source:

Lysobacter enzymogenes. Organism_taxid: 69. Synthetic: yes

Resolution:

2.10Å R-factor: 0.139

Authors:

R.Bone,D.A.Agard

Key ref:

R.Bone et al. (1989). Structural analysis of specificity: alpha-lytic protease complexes with analogues of reaction intermediates. Biochemistry, 28, 7600-7609. PubMed id: 2611204 DOI: 10.1021/bi00445a015

Date:

24-Apr-89 Release date: 15-Apr-90

Protein chain

P00778  (PRLA_LYSEN) -  Alpha-lytic protease from Lysobacter enzymogenes

Seq: 397 a.a.

Struc: 198 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.21.12 - alpha-lytic endopeptidase.
• Reaction: Hydrolysis of proteins, especially bonds adjacents to L-alanine and L-valine residues in bacterial cell walls, elastin and other proteins.

DOI no: 10.1021/bi00445a015

Biochemistry 28:7600-7609 (1989)

PubMed id: 2611204

Structural analysis of specificity: alpha-lytic protease complexes with analogues of reaction intermediates.

R.Bone, D.Frank, C.A.Kettner, D.A.Agard.

ABSTRACT

To better understand the structural basis of enzyme specificity, the structures of complexes formed between alpha-lytic protease, an extracellular serine protease of Lysobacter enzymogenes, and five inhibitory peptide boronic acids (R2-boroX, where R2 is methoxysuccinyl-Ala-Ala-Pro- and boroX is the alpha-aminoboronic acid analogue of Ala, Val, Ile, Norleu, or Phe) have been studied at high resolution by X-ray crystallography. The enzyme has primary specificity for Ala in the P1 position of peptide substrates with catalytic efficiency decreasing with increasing side-chain volume. Enzyme affinity for inhibitors with boroVal, boroIle, and boroPhe residues is much higher than expected on the basis of the catalytic efficiencies of homologous substrates. Covalent tetrahedral adducts are formed between the active-site serine and the boronic acid moieties of R2-boroAla, R2-boroVal R2-boroIle, and R2-boroNorleu. Though R2-boroVal is a slowly bound inhibitor and R2-boroAla is rapidly bound [Kettner, C. A., Bone, R., Agard, D. A., & Bachovchin, W. W. (1988) Biochemistry 27, 7682-7688], there appear to be no structural differences that could account for slow binding. The removal from solution of 20% more hydrophobic surface on binding accounts for the improved affinity of alpha-lytic protease for R2-boroVal relative to R2-boroAla. The high affinity of the enzyme for R2-boroIle derives from the selective binding of the L-allo stereoisomer of the boroIle residue, which can avoid bad steric interactions in the binding pocket.(ABSTRACT TRUNCATED AT 250 WORDS)