PDBsum entry 1fq7

Hydrolase/hydrolase inhibitor

PDB id: 1fq7

Contents

Protein chain

329 a.a. *

Ligands

NAG-NAG-BMA-BMA-KBG

2Y3

NAG

Waters ×65

* Residue conservation analysis

PDB id:

1fq7

Name:

Hydrolase/hydrolase inhibitor

Title:

X-ray structure of inhibitor cp-72,647 bound to saccharopepsin

Structure:

Saccharopepsin. Chain: a. Synonym: aspartate protease, proteinase a. Ec: 3.4.23.25

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932

Resolution:

2.80Å R-factor: 0.190 R-free: 0.270

Authors:

N.B.Cronin,M.O.Badasso,I.J.Tickle,T.Dreyer,D.J.Hoover,R.L.Rosati, C.C.Humblet,E.A.Lunney,J.B.Cooper

Key ref:

N.B.Cronin et al. (2000). X-ray structures of five renin inhibitors bound to saccharopepsin: exploration of active-site specificity. J Mol Biol, 303, 745-760. PubMed id: 11061973 DOI: 10.1006/jmbi.2000.4181

Date:

04-Sep-00 Release date: 20-Sep-00

Protein chain

P07267  (CARP_YEAST) -  Saccharopepsin from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 405 a.a.

Struc: 329 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.4.23.25 - saccharopepsin.
• Reaction: Hydrolysis of proteins with broad specificity for peptide bonds. Cleaves -Leu-Leu-|-Val-Tyr- bond in a synthetic substrate. Does not act on esters of Tyr or Arg.

DOI no: 10.1006/jmbi.2000.4181

J Mol Biol 303:745-760 (2000)

PubMed id: 11061973

X-ray structures of five renin inhibitors bound to saccharopepsin: exploration of active-site specificity.

N.B.Cronin, M.O.Badasso, I.J Tickle, T.Dreyer, D.J.Hoover, R.L.Rosati, C.C.Humblet, E.A.Lunney, J.B.Cooper.

ABSTRACT

Saccharopepsin is a vacuolar aspartic proteinase involved in activation of a number of hydrolases. The enzyme has great structural homology to mammalian aspartic proteinases including human renin and we have used it as a model system to study the binding of renin inhibitors by X-ray crystallography. Five medium-to-high resolution structures of saccharopepsin complexed with transition-state analogue renin inhibitors were determined. The structure of a cyclic peptide inhibitor (PD-129,541) complexed with the proteinase was solved to 2.5 A resolution. This inhibitor has low affinity for human renin yet binds very tightly to the yeast proteinase (K(i)=4 nM). The high affinity of this inhibitor can be attributed to its bulky cyclic moiety spanning P(2)-P(3)' and other residues that appear to optimally fit the binding sub-sites of the enzyme. Superposition of the saccharopepsin structure on that of renin showed that a movement of the loop 286-301 relative to renin facilitates tighter binding of this inhibitor to saccharopepsin. Our 2.8 A resolution structure of the complex with CP-108,420 shows that its benzimidazole P(3 )replacement retains one of the standard hydrogen bonds that normally involve the inhibitor's main-chain. This suggests a non-peptide lead in overcoming the problem of susceptible peptide bonds in the design of aspartic proteinase inhibitors. CP-72,647 which possesses a basic histidine residue at P(2), has a high affinity for renin (K(i)=5 nM) but proves to be a poor inhibitor for saccharopepsin (K(i)=3.7 microM). This may stem from the fact that the histidine residue would not bind favourably with the predominantly hydrophobic S(2) sub-site of saccharopepsin.

Selected figure(s)

Figure 5.
Figure 5. The charge distribution in the binding cavity of saccharopepsin bound to inhibitor PD-129,541. The red negatively charged "hot spot" indicates the position of the two catalytic aspartate residues. Inhibitor residues P[4] and P[3]' are seen emerging from the active site, while residues P[3] to P[2]' are buried. Residues of helix h[N]2 (111 to 114) interact with P[3], while residues of a hairpin structure (73 to 77) and the polyproline loop (residues M289-I300) enclose the inhibitor. This picture was prepared using GRASP [Nicholls et al 1993].

Figure 6.
Figure 6. A superposition of the saccharopepsin/inhibitor complexes: PD-129,541 (red); PD-133,450 (purple); CP-108,420 (aquamarine); CP-72,647 (green); CP-81,198 (blue) and CP-81,282 (grey). Their conformations are most conserved in the S[3] to S[1]' sub-sites.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 303, 745-760) copyright 2000.

Figures were selected by an automated process.