2FO5 | pdb_00002fo5

Crystal structure of recombinant barley cysteine endoprotease B isoform 2 (EP-B2) in complex with leupeptin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.233 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.202 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2FO5

This is version 1.5 of the entry. See complete history

Literature

Heterologous Expression, Purification, Refolding, and Structural-Functional Characterization of EP-B2, a Self-Activating Barley Cysteine Endoprotease.

Bethune, M.T.Strop, P.Tang, Y.Sollid, L.M.Khosla, C.

(2006) Chem Biol 13: 637-647

  • DOI: https://doi.org/10.1016/j.chembiol.2006.04.008
  • Primary Citation Related Structures: 
    2FO5

  • PubMed Abstract: 

    We describe the heterologous expression in Escherichia coli of the proenzyme precursor to EP-B2, a cysteine endoprotease from germinating barley seeds. High yields (50 mg/l) of recombinant proEP-B2 were obtained from E. coli inclusion bodies in shake flask cultures following purification and refolding. The zymogen was rapidly autoactivated to its mature form under acidic conditions at a rate independent of proEP-B2 concentration, suggesting a cis mechanism of autoactivation. Mature EP-B2 was stable and active over a wide pH range and efficiently hydrolyzed a recombinant wheat gluten protein, alpha2-gliadin, at sequences with known immunotoxicity in celiac sprue patients. The X-ray crystal structure of mature EP-B2 bound to leupeptin was solved to 2.2 A resolution and provided atomic insights into the observed subsite specificity of the endoprotease. Our findings suggest that orally administered proEP-B2 may be especially well suited for treatment of celiac sprue.


  • Organizational Affiliation
    • Department of Biochemistry, Stanford University, Stanford, California 94305, USA.

Macromolecule Content 

  • Total Structure Weight: 113.62 kDa 
  • Atom Count: 7,294 
  • Modeled Residue Count: 912 
  • Deposited Residue Count: 1,064 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cysteine proteinase EP-B 2
A, B, C, D
262Hordeum vulgareMutation(s): 0 
Gene Names: EPB2
EC: 3.4.22
UniProt
Find proteins for P25250 (Hordeum vulgare)
Explore P25250 
Go to UniProtKB:  P25250
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25250
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ACE-LEU-LEU-argininal (leupeptin)
E, F, G, H
4Streptomyces roseusMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
K [auth A]
L [auth B]
M [auth B]
I [auth A],
J [auth A],
K [auth A],
L [auth B],
M [auth B],
N [auth C],
O [auth C],
P [auth D],
Q [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
AR7
Query on AR7
E, F, G, H
PEPTIDE-LIKEC6 H17 N4 O2ARG

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.233 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.202 (DCC) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.37α = 86.32
b = 51.73β = 86.46
c = 115.655γ = 79.63
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-18
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2017-10-18
    Changes: Advisory, Refinement description
  • Version 1.5: 2024-11-20
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary