1APV

CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION STATE MIMICS BOUND TO PENICILLOPEPSIN: DIFLUOROSTATINE-AND DIFLUOROSTATONE-CONTAINING PEPTIDES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic analysis of transition state mimics bound to penicillopepsin: difluorostatine- and difluorostatone-containing peptides.

James, M.N.Sielecki, A.R.Hayakawa, K.Gelb, M.H.

(1992) Biochemistry 31: 3872-3886

  • Primary Citation of Related Structures:  1APW

  • PubMed Abstract: 
  • Difluorostatine- and difluorostatone-containing peptides have been evaluated as potent inhibitors of penicillopepsin, a member of the aspartic proteinase family of enzymes. Isovaleryl-Val-Val-StaF2NHCH3 [StaF2 = (S)-4-amino-2,2-difluoro-(R)-3-hydroxy ...

    Difluorostatine- and difluorostatone-containing peptides have been evaluated as potent inhibitors of penicillopepsin, a member of the aspartic proteinase family of enzymes. Isovaleryl-Val-Val-StaF2NHCH3 [StaF2 = (S)-4-amino-2,2-difluoro-(R)-3-hydroxy-6-methylheptanoic acid] and isovaleryl-Val-Val-StoF2NHCH3 [StoF2 = (S)-4-amino-2,2-difluoro-3-oxo-6-methylheptanoic acid] have measured Ki's of 10 x 10(-9) and 1 x 10(-9) M, respectively, with this fungal proteinase. The StoF2-containing peptide binds 32-fold more tightly to the enzyme than the analogous peptide containing the non-fluorinated statine ethyl ester. Each compound was cocrystallized with penicillopepsin, intensity data were collected to 1.8-A resolution, and the atomic coordinates were refined to an R factor [formula: see text] of 0.131 for both complexes. The inhibitors bind in the active site of penicillopepsin in much the same fashion as do other statine-containing inhibitors of penicillopepsin analyzed earlier [James, M. N. G., Sielecki, A. Salituro, F., Rich, D. H., & Hofmann, T. (1982) Proc. Natl. Acad. Sci. U.S.A. 79, 6137-6141; James, M.N.G., Sielecki, A., & Hofmann, T. (1985) in Aspartic Proteinases and their Inhibitors (Kosta, V., Ed.) pp 163-177, Walter deGruyter, Berlin]. The (R)-3-hydroxyl group in StaF2 binds between the active site carboxyl groups of Asp33 and Asp213, making hydrogen-bonding contacts to each one. The ketone functional group of the StoF2 inhibitor is bound as a hydrated species, with the gem-diol situated between the two aspartic acid carboxyl groups in a manner similar to that predicted for the tetrahedral intermediate expected during the catalytic hydrolysis of a peptide bond [James, M. N. G., & Sielecki, A. (1985) Biochemistry 24, 3701-3713]. One hydrogen-bonding interaction from the "outer" hydroxyl group is made to O delta 1 of Asp33, and the "inner" hydroxyl group forms two hydrogen-bonding contacts, one to each of the carboxyl groups of Asp33 (O delta 2) and Asp213 (O delta 2). The only structural difference between the StaF2 and StoF2 inhibitors that accounts for the factor of 10 in their Ki's is the additional (R)-3-OH group on the tetrahedral sp3 carbon atom of the hydrated StoF2 inhibitor. The intermolecular interactions involving the fluorine atoms of each inhibitor are normal van der Waals contacts to one of the carboxyl oxygen atoms of Asp213 (F2-O delta 2 Asp213, 2.9 A). The observed stereochemistry of the bound StoF2 group in the active site of penicillopepsin has stimulated our reappraisal of the catalytic pathway for the aspartic proteinases.(ABSTRACT TRUNCATED AT 400 WORDS)


    Related Citations: 
    • Aspartic Proteinases and Their Catalytic Pathway
      James, M.N.G.,Sielecki, A.R.
      (1987) Biological Macromolecules and Assemblies 3: 414
    • Stereochemical Analysis of Peptide Bond Hydrolysis Catalyzed by the Aspartic Proteinase Penicillopepsin
      James, M.N.G.,Sielecki, A.R.
      (1985) Biochemistry 24: 3701
    • Conformational Flexibility in the Active Sites of Aspartyl Proteinases Revealed by a Pepstatin Fragment Binding to Penicillopepsin
      James, M.N.G.,Sielecki, A.,Salituro, F.,Rich, D.H.,Hofmann, T.
      (1982) Proc.Natl.Acad.Sci.USA 79: 6137
    • Structure and Refinement of Penicillopepsin at 1.8 Angstroms Resolution
      James, M.N.G.,Sielecki, A.R.
      (1983) J.Mol.Biol. 163: 299
    • X-Ray Diffraction Studies on Penicillopepsin and its Complexes: The Hydrolytic Mechanism
      James, M.N.G.,Sielecki, A.R.,Hofmann, T.
      (1985) Aspartic Proteinases and Their Inhibitors --: 163
    • Effect of Ph on the Activities of Penicillopepsin and Rhizopus Pepsin and a Proposal for the Productive Substrate Binding Mode in Penicillopepsin
      Hofmann, T.,Hodges, R.S.,James, M.N.G.
      (1984) Biochemistry 23: 635
    • Crystallographic Analysis of a Pepstatin Analogue Binding to the Aspartyl Proteinase Penicillopepsin at 1.8 Angstroms Resolution
      James, M.N.G.,Sielecki, A.R.,Moult, J.
      (1983) Peptides: Structure and Function, Proceedings of the of the Eighth American Peptide Symposium --: 521


    Organizational Affiliation

    Department of Biochemistry, University of Alberta, Edmonton, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PENICILLOPEPSIN
E
323Penicillium janthinellumEC: 3.4.23.20
Find proteins for P00798 (Penicillium janthinellum)
Go to UniProtKB:  P00798
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
INHIBITOR ISOVALERYL (IVA)-VAL-VAL-HYDRATED DIFLUOROSTATONE-N-METHYLAMINE
I
5N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
E
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
XYS
Query on XYS

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Download CCD File 
E
XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-LECHCGJUSA-N
 Ligand Interaction
DMF
Query on DMF

Download SDF File 
Download CCD File 
I
DIMETHYLFORMAMIDE
C3 H7 N O
ZMXDDKWLCZADIW-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
DFO
Query on DFO
I
L-PEPTIDE LINKINGC8 H15 F2 N O4

--

NME
Query on NME
I
NON-POLYMERC H5 N

--

IVA
Query on IVA
I
NON-POLYMERC5 H10 O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 97.520α = 90.00
b = 46.570β = 116.03
c = 66.230γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    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