1PPK

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


Experimental Data Snapshot

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

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:  1PPL, 1PPM

  • 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: 
    • Aspartic Proteinases and Their Catalytic Pathway
      James, M.N.G.,Sielecki, A.R.
      (1987) Biological Macromolecules and Assemblies 3: 414
    • 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
    • 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
    • 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
    • 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
    • Stereochemical Analysis of Peptide Bond Hydrolysis Catalyzed by the Aspartic Proteinase Penicillopepsin
      James, M.N.G.,Sielecki, A.R.
      (1985) Biochemistry 24: 3701
    • Crystallographic Analysis of Transition State Mimics Bound to Penicillopepsin: Difluorostatine-and Difluorostatone-Containing Peptides
      James, M.N.G.,Sielecki, A.R.,Hayakawa, K.,Gelb, M.H.
      (1992) Biochemistry 31: 3872


    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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HSY
Query on HSY

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Download CCD File 
E
alpha-L-xylopyranose
C5 H10 O5
SRBFZHDQGSBBOR-SKNVOMKLSA-N
 Ligand Interaction
SO4
Query on SO4

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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
DMF
Query on DMF

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Download CCD File 
E
DIMETHYLFORMAMIDE
C3 H7 N O
ZMXDDKWLCZADIW-UHFFFAOYSA-N
 Ligand Interaction
IVV
Query on IVV

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Download CCD File 
E
N-(3-methylbutanoyl)-L-valyl-N-{(1R)-1-[(R)-(2-ethoxy-2-oxoethyl)(hydroxy)phosphoryl]-3-methylbutyl}-L-valinamide
PHOSPHINIC ACID ANALOGUE OF STATIN (IVA)-VAL-VAL-STA(P)-O-ET
C24 H46 N3 O7 P
GSDBAIBPJKAZKN-HJNYFJLDSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000664 (IVV)
Query on PRD_000664
Eisovaleryl (IVA)-VAL-VAL-STA(P)-O-ET phosphinic acid analogue of statinPeptide-like / Inhibitor

--

External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IVVKi: 22 nM BINDINGMOAD
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 = 97.480α = 90.00
b = 46.550β = 116.14
c = 66.420γ = 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: 1994-05-31
    Type: Initial release
  • Version 1.1: 2008-05-22
    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