Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37818.70 
• Atom Count: 2665 
• Residue Count: 329 
• Unique protein chains: 1

1FQ5

X-ray structure of a cyclic statine inhibitor PD-129,541 bound to yeast proteinase A

• DOI: 10.2210/pdb1FQ5/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Saccharomyces cerevisiae (strain ATCC 204508 / S288c)


• Deposited: 2000-09-03 Released: 2000-09-20 
• Deposition Author(s): Cronin, N.B., Badasso, M.O., Tickle, I.J., Dreyer, T., Hoover, D.J., Rosati, R.L., Humblet, C.C., Lunney, E.A., Cooper, J.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.280 

Literature

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

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

(2000) J.Mol.Biol. 303: 745-760

• PubMed: 11061973 
• DOI: 10.1006/jmbi.2000.4181
• Primary Citation of Related Structures:  
  1FQ8, 1FQ7, 1FQ6, 1FQ4


• PubMed 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.

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Related Citations: 

• The Three-dimensional Structure at 2.4 A Resolution of Glycosylated Proteinase A from the Lysosome-like Vacuole of Saccharomyces cerevisiae
  Aguilar, C.F.,Cronin, N.B.,Badasso, M.,Dreyer, T.,Newman, M.P.,Cooper, J.B.,Hoover, D.J.,Wood, S.P.,Johnson, M.S.,Blundell, T.L.
  (1997) J.Mol.Biol. 267: 899




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Organizational Affiliation: 

Department of Crystallography, Birkbeck College, University of London, London, WC1E 7HX, UK.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
SACCHAROPEPSIN	A	329	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: PEP4 (PHO9, PRA1) EC: 3.4.23.25
Find proteins for P07267 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P07267

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MAN	A	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BMA	A	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
0GM	A	N-[(5S,9S,10S,13S)-9-hydroxy-5,10-bis(2-methylpropyl)-4,7,12,16-tetraoxo-3,6,11,17-tetraazabicyclo[17.3.1]tricosa-1(23),19,21-trien-13-yl]-3-(naphthalen-1-yl)-2-(naphthalen-1-ylmethyl)propanamide CP-129,541 C51 H61 N5 O6 KFCMUWOMPCWWCH-AXYJRABVSA-N
NDG	A	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
0GM	Ki: 4 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.280 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 87.300	α = 90.00
b = 87.300	β = 90.00
c = 110.700	γ = 120.00

Software Package:

Software Name	Purpose
RESTRAIN	refinement
ROTAVATA	data scaling
CCP4	data scaling
ROTAVATA	data reduction
AMoRE	phasing
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-09-03 
• Released Date: 2000-09-20 
• Deposition Author(s): Cronin, N.B., Badasso, M.O., Tickle, I.J., Dreyer, T., Hoover, D.J., Rosati, R.L., Humblet, C.C., Lunney, E.A., Cooper, J.B.

Revision History 

• Version 1.0: 2000-09-20
  Type: Initial release
• Version 1.1: 2008-04-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2016-12-14
  Type: Structure summary
• Version 1.4: 2017-10-04
  Type: Refinement description