PDBsum entry 2bd4

Hydrolase

PDB id: 2bd4

Contents

Protein chain

240 a.a. *

Ligands

ILE-LYS

SO4

Metals

_CA

Waters ×100

* Residue conservation analysis

PDB id:

2bd4

Name:

Hydrolase

Title:

Porcine pancreatic elastase complexed with beta-casomorphin-7 and lys- ser at ph 5.0

Structure:

Beta-casomorphin-7. Chain: p. Engineered: yes. Other_details: last aa is a part of nucleophilic dipeptides. Chymotrypsin-like elastase family member 1. Chain: a. Synonym: elastase-1. Ec: 3.4.21.36

Source:

Synthetic: yes. Homo sapiens. Organism_taxid: 9606. Other_details: synthetic peptide. Sus scrofa. Pig. Organism_taxid: 9823

Resolution:

1.70Å R-factor: 0.188 R-free: 0.220

Authors:

B.Liu,C.J.Schofield,R.C.Wilmouth

Key ref:

B.Liu et al. (2006). Structural analyses on intermediates in serine protease catalysis. J Biol Chem, 281, 24024-24035. PubMed id: 16754679 DOI: 10.1074/jbc.M600495200

Date:

20-Oct-05 Release date: 30-May-06

Protein chain

P00772  (CELA1_PIG) -  Chymotrypsin-like elastase family member 1 from Sus scrofa

Seq: 266 a.a.

Struc: 240 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.4.21.36 - pancreatic elastase.
• Reaction: Hydrolysis of proteins, including elastin. Preferential cleavage: Ala-|-Xaa.

DOI no: 10.1074/jbc.M600495200

J Biol Chem 281:24024-24035 (2006)

PubMed id: 16754679

Structural analyses on intermediates in serine protease catalysis.

B.Liu, C.J.Schofield, R.C.Wilmouth.

ABSTRACT

Although the subject of many studies, detailed structural information on aspects of the catalytic cycle of serine proteases is lacking. Crystallographic analyses were performed in which an acyl-enzyme complex, formed from elastase and a peptide, was reacted with a series of nucleophilic dipeptides. Multiple analyses led to electron density maps consistent with the formation of a tetrahedral species. In certain cases, apparent peptide bond formation at the active site was observed, and the electron density maps suggested production of a cis-amide rather than a trans-amide. Evidence for a cis-amide configuration was also observed in the noncovalent complex between elastase and an alpha1-antitrypsin-derived tetrapeptide. Although there are caveats on the relevance of the crystallographic data to solution catalysis, the results enable detailed proposals for the pathway of the acylation step to be made. At least in some cases, it is proposed that the alcohol of Ser-195 may preferentially attack the carbonyl of the cis-amide form of the substrate, in a stereoelectronically favored manner, to give a tetrahedral oxyanion intermediate, which undergoes N-inversion and/or C-N bond rotation to enable protonation of the leaving group nitrogen. The mechanistic proposals may have consequences for protease inhibition, in particular for the design of high energy intermediate analogues.

Selected figure(s)

Figure 3.
FIGURE 3. Stereoviews of the active site of PPE complexed with BCM7 and different dipeptides showing the results of the pH jump (pH 9, 30s) of the Lys-Ser structure shown in Fig. 1b (a) and the results of the pH jumps of the Arg-Phe structure shown in Fig. 2d (one pH jump (pH 9, 30 s) (b) and a second pH jump (pH 9, 28 s) (c)). The color scheme and contouring levels for the atoms and maps are as in Fig. 1a. The resolution of the structures is 1.8, 1.7, and 1.9 Å, respectively.

Figure 5.
FIGURE 5. Two proposed forms of the first tetrahedral intermediate (A and B) interchangeable via N-inversion and/or rotation about the C-N bond. In A, the P1' nitrogen lone pair projects away from His-57, and in B it projects toward it. In intermediate B, R and R' refer to either hydrogen or the P1' residue, depending on whether N-inversion has occurred. The amide nitrogen of Ser-195, which forms part of the oxyanion hole, is not shown for clarity; from the viewpoint shown, it lies behind the plane of the picture. Note that steric constraints mean that the conformation in which the nitrogen lone pair is exactly coplanar with the C-O(Ser-195) bond is unlikely.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 24024-24035) copyright 2006.

Figures were selected by an automated process.