1PPM

CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION-STATE MIMICS BOUND TO PENICILLOPEPSIN: PHOSPHORUS-CONTAINING PEPTIDE ANALOGUES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystallographic analysis of transition-state mimics bound to penicillopepsin: phosphorus-containing peptide analogues.

Fraser, M.E.Strynadka, N.C.Bartlett, P.A.Hanson, J.E.James, M.N.

(1992) Biochemistry 31: 5201-5214

  • Primary Citation of Related Structures:  1PPK, 1PPL

  • PubMed Abstract: 
  • The molecular structures of three phosphorus-based peptide inhibitors of aspartyl proteinases complexed with penicillopepsin [1, Iva-L-Val-L-Val-StaPOEt [Iva = isovaleryl, StaP = the phosphinic acid analogue of statine [(S)-4-amino-(S)-3-hydroxy-6-me ...

    The molecular structures of three phosphorus-based peptide inhibitors of aspartyl proteinases complexed with penicillopepsin [1, Iva-L-Val-L-Val-StaPOEt [Iva = isovaleryl, StaP = the phosphinic acid analogue of statine [(S)-4-amino-(S)-3-hydroxy-6-methylheptanoic acid] (IvaVVStaPOEt)]; 2, Iva-L-Val-L-Val-L-LeuP-(O)Phe-OMe [LeuP = the phosphinic acid analogue of L-leucine; (O)Phe = L-3-phenyllactic acid; OMe = methyl ester] [Iva VVLP(O)FOMe]; and 3, Cbz-L-Ala-L-Ala-L-LeuP-(O)-Phe-OMe (Cbz = benzyloxycarbonyl) [CbzAALP(O)FOMe]] have been determined by X-ray crystallography and refined to crystallographic agreement factors, R ( = sigma parallel to F0 magnitude of - Fc parallel to/sigma magnitude of F0), of 0.132, 0.131, and 0.134, respectively. These inhibitors were designed to be structural mimics of the tetrahederal transition-state intermediate encountered during aspartic proteinase catalysis. They are potent inhibitors of penicillopepsin with Ki values of 1, 22 nM; 2, 2.8 nM; and 3, 1600 nM, respectively [Bartlett, P. A., Hanson, J. E., & Giannousis, P. P. (1990) J. Org. Chem. 55, 6268-6274]. All three of these phosphorus-based inhibitors bind virtually identically in the active site of penicillopepsin in a manner that closely approximates that expected for the transition state [James, M. N. G., Sielecki, A.R., Hayakawa, K., & Gelb, M. H. (1992) Biochemistry 31, 3872-3886]. The pro-S oxygen atom of the two phosphonate inhibitors and of the phosphinate group of the StaP inhibitor make very short contact distances (approximately 2.4 A) to the carboxyl oxygen atom, O delta 1, of Asp33 on penicillopepsin. We have interpreted this distance and the stereochemical environment of the carboxyl and phosphonate groups in terms of a hydrogen bond that most probably has a symmetric single-well potential energy function. The pro-R oxygen atom is the recipient of a hydrogen bond from the carboxyl group of Asp213. Thus, we are able to assign a neutral status to Asp213 and a partially negatively charged status to Asp33 with reasonable confidence. Similar very short hydrogen bonds involving the active site glutamic acid residues of thermolysin and carboxypeptidase A and the pro-R oxygen of bound phosphonate inhibitors have been reported [Holden, H. M., Tronrud, D. E., Monzingo, A. F., Weaver, L. H., & Matthews, B. W. (1987) Biochemistry 26, 8542-8553; Kim, H., & Lipscomb, W. N. (1991) Biochemistry 30, 8171-8180].(ABSTRACT TRUNCATED AT 400 WORDS)


    Related Citations: 
    • Structure and Refinement of Penicillopepsin at 1.8 Angstroms Resolution
      James, M.N.G.,Sielecki, A.R.
      (1983) J.Mol.Biol. 163: 299
    • An X-Ray Crystallographic Approach to Enzyme Structure and Function
      James, M.N.G.
      (1980) Can.J.Biochem. 58: 251
    • Aspartic Proteinases and Their Catalytic Pathway
      James, M.N.G.,Sielecki, A.R.
      (1987) Biological Macromolecules and Assemblies 3: 413
    • Structural Evidence for Gene Duplication in the Evolution of the Acid Proteases
      Tang, J.,James, M.N.G.,Hsu, I.N.,Jenkins, J.A.,Blundell, T.L.
      (1978) Nature 271: 618
    • The Tertiary Structure of Penicillopepsin. Towards a Catalytic Mechanism for Acid Proteases
      James, M.N.G.,Hsu, I-N.,Hofmann, T.,Sielecki, A.R.
      (1981) STRUCTURAL STUDIES ON MOLECULES OF BIOLOGICA INTERESTL --: 350
    • 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
    • The Crystal Structure of Penicillopepsin at 6 Angstroms Resolution
      Hsu, I-N.,Hofmann, T.,Nyburg, S.C.,James, M.N.G.
      (1976) Biochem.Biophys.Res.Commun. 72: 363
    • Penicillopepsin. 2.8 Angstroms Structure, Active Site Conformation and Mechanistic Implications
      Hsu, I-N.,Delbaere, L.T.J.,James, M.N.G.,Hofmann, T.
      (1977) Adv.Exp.Med.Biol. 95: 61
    • Stereochemical Analysis of Peptide Bond Hydrolysis Catalyzed by the Aspartic Proteinase Penicillopepsin
      James, M.N.G.,Sielecki, A.R.
      (1985) Biochemistry 24: 3701
    • Penicillopepsin from Penicillium Janthinellum Crystal Structure at 2.8 Angstroms and Sequence Homology with Porcine Pepsin
      Hsu, I.-N.,Delbaere, L.T.J.,James, M.N.G.,Hofmann, T.
      (1977) Nature 266: 140
    • Mechanism of Acid Protease Catalysis Based on the Crystal Structure of Penicillopepsin
      James, M.N.G.,Hsu, I.-N.,Delbaere, L.T.J.
      (1977) Nature 267: 808


    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
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0P1
Query on 0P1

Download SDF File 
Download CCD File 
E
N-[(benzyloxy)carbonyl]-L-alanyl-N-{(1S)-1-[(R)-[(1R)-1-benzyl-2-methoxy-2-oxoethoxy](hydroxy)phosphoryl]-3-methylbutyl}-L-alaninamide
Cbz-Ala-Ala-Leu(P)-(O)-Phe-OMe
C29 H40 N3 O9 P
VWCUANLUSQBJLX-WIHVIGOGSA-N
 Ligand Interaction
ARA
Query on ARA

Download SDF File 
Download CCD File 
E
ALPHA-L-ARABINOSE
C5 H10 O5
SRBFZHDQGSBBOR-QMKXCQHVSA-N
 Ligand Interaction
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
E
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000328 (0P1)
Query on PRD_000328
ECbz-Ala-Ala-Leu(P)-(O)-Phe-OMePeptide-like / Inhibitor

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0P1Ki: 1600 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Work: 0.150 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 97.400α = 90.00
b = 46.590β = 115.70
c = 66.290γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    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: 2012-12-12
    Type: Other