PDBsum entry 2foa

Hydrolase

PDB id: 2foa

Contents

Protein chain

240 a.a. *

Ligands

SO4

IPA ×3

Metals

_CA

Waters ×161

* Residue conservation analysis

PDB id:

2foa

Name:

Hydrolase

Title:

Structure of porcine pancreatic elastase in 40/50/10 % benzene

Structure:

Elastase-1. Chain: a. Synonym: pancreatic elastase. Ec: 3.4.21.36

Source:

Sus scrofa. Pig. Organism_taxid: 9823. Organ: pancreas

Resolution:

1.90Å R-factor: 0.161 R-free: 0.200

Authors:

C.Mattos,C.R.Bellamacina,E.Peisach,A.Pereira,D.Vitkup,G.A.Petsko, D.Ringe

Key ref:

C.Mattos et al. (2006). Multiple solvent crystal structures: probing binding sites, plasticity and hydration. J Mol Biol, 357, 1471-1482. PubMed id: 16488429 DOI: 10.1016/j.jmb.2006.01.039

Date:

13-Jan-06 Release date: 18-Apr-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: 10.1016/j.jmb.2006.01.039

J Mol Biol 357:1471-1482 (2006)

PubMed id: 16488429

Multiple solvent crystal structures: probing binding sites, plasticity and hydration.

C.Mattos, C.R.Bellamacina, E.Peisach, A.Pereira, D.Vitkup, G.A.Petsko, D.Ringe.

ABSTRACT

Multiple solvent crystal structures (MSCS) of porcine pancreatic elastase were used to map the binding surface the enzyme. Crystal structures of elastase in neat acetonitrile, 95% acetone, 55% dimethylformamide, 80% 5-hexene-1,2-diol, 80% isopropanol, 80% ethanol and 40% trifluoroethanol showed that the organic solvent molecules clustered in the active site, were found mostly unclustered in crystal contacts and in general did not bind elsewhere on the surface of elastase. Mixtures of 40% benzene or 40% cyclohexane in 50% isopropanol and 10% water showed no bound benzene or cyclohexane molecules, but did reveal bound isopropanol. The clusters of organic solvent probe molecules coincide with pockets occupied by known inhibitors. MSCS also reveal the areas of plasticity within the elastase binding site and allow for the visualization of a nearly complete first hydration shell. The pattern of organic solvent clusters determined by MSCS for elastase is consistent with patterns for hot spots in protein-ligand interactions determined from database analysis in general. The MSCS method allows probing of hot spots, plasticity and hydration simultaneously, providing a powerful complementary strategy to guide computational methods currently in development for binding site determination, ligand docking and design.

Selected figure(s)

Figure 1.
Figure 1. Organic solvent binding sites. Ribbon diagram of elastase showing the binding sites for organic solvent molecules in a common frame of reference. Each site is numbered as described in the text. The number of the sites occupied by organic solvent molecules in each of the models is given in Table 2. The catalytic triad is shown explicitly in the cleft between the two b-barrel domains: Ser203, His60, Asp108 are shown in gray. The b-strands are shown in purple and the two a-helices are shown in green. The organic solvent molecules are color-coded as follows: HEX, salmon; ETH, hot pink; TFE1, cyan; TFE2, orange; IPR, light green; IBZ, green; ICY, dark green; ACE, red; DMF, blue; ACN, yellow. Figure 1, Figure 2, Figure 3 and Figure 4 were made using the program MOLSCRIPT.52

Figure 4.
Figure 4. Crystallographic water molecules in the active site. The same region of the active site is shown as in Figure 2 and Figure 3, with the same color code for protein atoms and organic solvent molecules. Water molecules are superimposed on the trifluoroactyl-Lys-Pro-p-isopropylanilide (pink). The water molecules are color-coded according to the model from which they were taken: XLINK, white; HEX, salmon; ETH, hot pink; TFE1, cyan; TFE2, orange; IPR, light green; IBZ, green; ICY, dark green; ACE, red; DMF, blue; ACN, yellow.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 357, 1471-1482) copyright 2006.

Figures were selected by an automated process.