1QDM

CRYSTAL STRUCTURE OF PROPHYTEPSIN, A ZYMOGEN OF A BARLEY VACUOLAR ASPARTIC PROTEINASE.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of plant aspartic proteinase prophytepsin: inactivation and vacuolar targeting.

Kervinen, J.Tobin, G.J.Costa, J.Waugh, D.S.Wlodawer, A.Zdanov, A.

(1999) EMBO J. 18: 3947-3955

  • DOI: 10.1093/emboj/18.14.3947

  • PubMed Abstract: 
  • We determined at 2.3 A resolution the crystal structure of prophytepsin, a zymogen of a barley vacuolar aspartic proteinase. In addition to the classical pepsin-like bilobal main body of phytepsin, we also traced most of the propeptide, as well as an ...

    We determined at 2.3 A resolution the crystal structure of prophytepsin, a zymogen of a barley vacuolar aspartic proteinase. In addition to the classical pepsin-like bilobal main body of phytepsin, we also traced most of the propeptide, as well as an independent plant-specific domain, never before described in structural terms. The structure revealed that, in addition to the propeptide, 13 N-terminal residues of the mature phytepsin are essential for inactivation of the enzyme. Comparison of the plant-specific domain with NK-lysin indicates that these two saposin-like structures are closely related, suggesting that all saposins and saposin-like domains share a common topology. Structural analysis of prophytepsin led to the identification of a putative membrane receptor-binding site involved in Golgi-mediated transport to vacuoles.


    Organizational Affiliation

    Protein Structure Section, Macromolecular Structure Laboratory, ABL-Basic Research Program, NCI-Frederick Cancer Research and Development Center, Frederick, MD 21702, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROPHYTEPSIN
A, B, C
478Hordeum vulgareMutation(s): 0 
EC: 3.4.23.40
Find proteins for P42210 (Hordeum vulgare)
Go to UniProtKB:  P42210
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 66.000α = 90.00
b = 160.900β = 109.60
c = 81.400γ = 90.00
Software Package:
Software NamePurpose
CCP4phasing
DENZOdata reduction
PHASESphasing
AMoREphasing
X-PLORrefinement
CCP4model building
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-07-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance