PDBsum entry 1gvk

Hydrolase/hydrolase inhibitor

PDB id: 1gvk

Contents

Protein chain

240 a.a. *

Ligands

ACE-ASN-PRO-ILE

SO4 ×2

Metals

_CA

Waters ×331

* Residue conservation analysis

PDB id:

1gvk

Name:

Hydrolase/hydrolase inhibitor

Title:

Porcine pancreatic elastase acyl enzyme at 0.95 a resolution

Structure:

Peptide inhibitor. Chain: a. Synonym: n-ac-npi-co2h. Engineered: yes. Elastase 1. Chain: b. Ec: 3.4.21.36

Source:

Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Other_details: related to beta-casomorphin. Sus scrofa. Pig. Organism_taxid: 9823. Organ: pancreas. Tissue: gland.

Resolution:

0.94Å R-factor: 0.122 R-free: 0.147

Authors:

G.Katona,R.C.Wilmouth,P.A.Wright,G.I.Berglund,J.Hajdu,R.Neutze, C.J.Schofield

Key ref:

G.Katona et al. (2002). X-ray structure of a serine protease acyl-enzyme complex at 0.95-A resolution. J Biol Chem, 277, 21962-21970. PubMed id: 11896054 DOI: 10.1074/jbc.M200676200

Date:

14-Feb-02 Release date: 19-Jul-02

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.M200676200

J Biol Chem 277:21962-21970 (2002)

PubMed id: 11896054

X-ray structure of a serine protease acyl-enzyme complex at 0.95-A resolution.

G.Katona, R.C.Wilmouth, P.A.Wright, G.I.Berglund, J.Hajdu, R.Neutze, C.J.Schofield.

ABSTRACT

Kinetic analyses led to the discovery that N-acetylated tripeptides with polar residues at P3 are inhibitors of porcine pancreatic elastase (PPE) that form unusually stable acyl-enzyme complexes. Peptides terminating in a C-terminal carboxylate were more potent than those terminating in a C-terminal amide, suggesting recognition by the oxy-anion hole is important in binding. X-ray diffraction data were recorded to 0.95-A resolution for an acyl-enzyme complex formed between PPE and N-acetyl-Asn-Pro-Ile-CO2H at approximately pH 5. The accuracy of the crystallographic coordinates allows structural issues concerning the mechanism of serine proteases to be addressed. Significantly, the ester bond of the acyl-enzyme showed a high level of planarity, suggesting geometric strain of the ester link is not important during catalysis. Several hydrogen atoms could be clearly identified and were included within the model. In keeping with a recent x-ray structure of subtilisin at 0.78 A (1), limited electron density is visible consistent with the putative location of a hydrogen atom approximately equidistant between the histidine and aspartate residues of the catalytic triad. Comparison of this high resolution crystal structure of the acyl-enzyme complex with that of native elastase at 1.1 A (2) showed that binding of the N-terminal part of the substrate can be accommodated with negligible structural rearrangements. In contrast, comparison with structures obtained as part of "time-resolved" studies on the reacting acyl-enzyme complex at >pH 7 (3) indicate small but significant structural differences, consistent with the proposed synchronization of ester hydrolysis and substrate release.

Selected figure(s)

Figure 1.
Fig. 1. Structure and electron density for the acyl-intermediate near the substrate binding cleft at 0. 95-Å resolution. A, 2F[obs] F[calc] electron density map contoured to 1.7 (blue) and 4.0 (gold). The blue contour level was chosen such that atoms with 60% occupancy become visible in the active site. The structural model for the enzyme moiety is green, with the exception of the oxygen and nitrogen atoms of the catalytic histidine and serine, which are colored red and blue, respectively. The acyl-peptide moiety is colored orange. B, least square superposition of the 0.95-Å acyl-intermediate structure (cyan) and the 1.1-Å native elastase structure (green).

Figure 2.
Fig. 2. Detailed view of the ester bond and the oxy-anion hole. A, stereo representation illustrating the degree of pyramidal distortion of the ester bond. The transparent plane passes through the carbonyl oxygen of the ester bond, the C[ ]of Ile-7, and O[ ]of Ser-195. The displacement of the carbonyl carbon of the ester bond from this plane is 0.05 Å. B, ball-and-stick representation of the enzymatic ester bond within the oxy-anion hole. The naming convention in Table III is used to identify atoms. C, ball-and-stick representation of the ethyl-acetate structure, providing an example of a small molecular ester.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 21962-21970) copyright 2002.

Figures were selected by an automated process.