1LYW

CATHEPSIN D AT PH 7.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Conformational switching in an aspartic proteinase.

Lee, A.Y.Gulnik, S.V.Erickson, J.W.

(1998) Nat.Struct.Mol.Biol. 5: 866-871

  • DOI: 10.1038/2306

  • PubMed Abstract: 
  • The crystal structure of a catalytically inactive form of cathepsin D (CatDhi) has been obtained at pH 7.5. The N-terminal strand relocates by 30 A from its position in the interdomain beta-sheet and inserts into the active site cleft, effectively bl ...

    The crystal structure of a catalytically inactive form of cathepsin D (CatDhi) has been obtained at pH 7.5. The N-terminal strand relocates by 30 A from its position in the interdomain beta-sheet and inserts into the active site cleft, effectively blocking substrate access. CatDhi has a five-stranded interdomain beta-sheet and resembles Intermediate 3, a hypothetical structure proposed to be transiently formed during proteolytic activation of the proenzyme precursor. Interconversion between active and inactive forms of CatD is reversible and may be regulated by an ionizable switch involving the carboxylate side chains of Glu 5, Glu 180, and Asp 187. Our findings provide a structural basis for the pH-dependent regulation of aspartic proteinase activity and suggest a novel mechanism for pH-dependent modulation of substrate specificity.


    Related Citations: 
    • Crystal Structures of Native and Inhibited Forms of Human Cathepsin D: Implications for Lysosomal Targeting and Drug Design
      Baldwin, E.T.,Bhat, T.N.,Gulnik, S.,Hosur, M.V.,Sowder II, R.C.,Cachau, R.E.,Collins, J.,Silva, A.M.,Erickson, J.W.
      (1993) Proc.Natl.Acad.Sci.USA 90: 6796
    • Human Liver Cathepsin D. Purification, Crystallization and Preliminary X-Ray Diffraction Analysis of a Lysosomal Enzyme
      Gulnik, S.,Baldwin, E.T.,Tarasova, N.,Erickson, J.
      (1992) J.Mol.Biol. 227: 265


    Organizational Affiliation

    Structural Biochemistry Program, SAIC Frederick, National Cancer Institute, Maryland 21702-1201, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CATHEPSIN D
A, C, E, G
97Homo sapiensGene Names: CTSD (CPSD)
EC: 3.4.23.5
Find proteins for P07339 (Homo sapiens)
Go to Gene View: CTSD
Go to UniProtKB:  P07339
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CATHEPSIN D
B, D, F, H
241Homo sapiensGene Names: CTSD (CPSD)
EC: 3.4.23.5
Find proteins for P07339 (Homo sapiens)
Go to Gene View: CTSD
Go to UniProtKB:  P07339
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A, C, E, G
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 140.256α = 90.00
b = 136.797β = 90.00
c = 140.416γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
DENZOdata reduction
X-PLORrefinement
SCALEPACKdata scaling
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-07-22
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance