1GVK

Porcine pancreatic elastase acyl enzyme at 0.95 A resolution

Summary for 1GVK

• Entry DOI: 10.2210/pdb1gvk/pdb
• Related: 1B0E 1BMA 1BTU 1C1M 1E34 1E35 1E36 1E37 1E38 1E9H 1EAI 1EAS 1EAT 1EAU 1ELA 1ELB 1ELC 1ELD 1ELE 1ELF 1ELG 1ESA 1ESB 1EST 1FLE 1FZZ 1H9L 1HAX 1HAY 1HAZ 1HB0 1HV7 1INC 1JIM 1LVY 1NES 1QGF 1QIX 1QNJ 1QR3 2EST 3EST 4EST 5EST 6EST 7EST 8EST 9EST
• Descriptor: PEPTIDE INHIBITOR, ELASTASE 1, SULFATE ION, ... (5 entities in total)
• Functional Keywords: hydrolase, serine protease, catalytic intermediate, atomic resolution, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: SUS SCROFA (PIG); More
• Total number of polymer chains: 2
• Total formula weight: 26528.66

Authors

Katona, G.,Wilmouth, R.C.,Wright, P.A.,Berglund, G.I.,Hajdu, J.,Neutze, R.,Schofield, C.J. (deposition date: 2002-02-14, release date: 2002-07-19, Last modification date: 2024-10-09)

Primary citation

Katona, G.,Wilmouth, R.C.,Wright, P.A.,Berglund, G.I.,Hajdu, J.,Neutze, R.,Schofield, C.J.
X-Ray Structure of a Serine Protease Acyl-Enzyme Complex at 0.95-A Resolution.
J.Biol.Chem., 277:21962-, 2002

PubMed 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.

PubMed: 11896054
DOI: 10.1074/JBC.M200676200

Experimental method

X-RAY DIFFRACTION (0.94 Å)