1QDM | pdb_00001qdm

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 
    0.224 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1QDM

This is version 1.3 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: https://doi.org/10.1093/emboj/18.14.3947
  • Primary Citation Related Structures: 
    1QDM

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 153.99 kDa 
  • Atom Count: 9,336 
  • Modeled Residue Count: 1,297 
  • Deposited Residue Count: 1,434 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROPHYTEPSIN
A, B, C
478Hordeum vulgareMutation(s): 0 
EC: 3.4.23.40
Membrane Entity: Yes 
UniProt
Find proteins for P42210 (Hordeum vulgare)
Explore P42210 
Go to UniProtKB:  P42210
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42210
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work:  0.224 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66α = 90
b = 160.9β = 109.6
c = 81.4γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CCP4model building
X-PLORrefinement
CCP4phasing
PHASESphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-07-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary