1BRY

BRYODIN TYPE I RIP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular, biological, and preliminary structural analysis of recombinant bryodin 1, a ribosome-inactivating protein from the plant Bryonia dioica.

Gawlak, S.L.Neubauer, M.Klei, H.E.Chang, C.Y.Einspahr, H.M.Siegall, C.B.

(1997) Biochemistry 36: 3095-3103

  • DOI: 10.1021/bi962474+

  • PubMed Abstract: 
  • Bryonia dioica (Cucurbitaceae family) produces at least two type I ribosome-inactivating proteins, bryodin 1 (BD1) and bryodin 2 (BD2). A cDNA sequence encoding BD1 was isolated from B. dioica leaf mRNA using degenerative oligonucleotides and codes f ...

    Bryonia dioica (Cucurbitaceae family) produces at least two type I ribosome-inactivating proteins, bryodin 1 (BD1) and bryodin 2 (BD2). A cDNA sequence encoding BD1 was isolated from B. dioica leaf mRNA using degenerative oligonucleotides and codes for a 22 amino acid signal peptide followed by a protein of 267 residues. Expression of two recombinant BD1 (rBD1) forms in Escherichia coli yielded proteins of 267 (to the natural stop codon) and 247 amino acids (to the putative cleavage site yielding the mature protein) that had identical protein synthesis inhibition activity as compared to native BD1. The substitution of Lys for Glu at position 189 near the active site reduced the ability of rBD1 to inhibit protein synthesis by 10-fold. Toxicologic analysis showed that rBD1 was well tolerated in rodents with LD50 values of 40 mg/kg in mice and >25 mg/kg in rats. A crystal of mature rBD1 protein was used to collect X-ray diffraction data to 2.1 A resolution. The rBD1 crystal structure was solved and showed extensive homology with other type I RIPs and A chains of type II RIPs. The studies described here demonstrate that rBD1 retains full biologic activity and serve as a guide for using this potent, yet nontoxic, RIP in the construction of single-chain immunotoxin fusion proteins.


    Related Citations: 
    • Characterization of Ribosome-Inactivating Proteins Isolated from Bryonia Dioica and Their Utility as Carcinoma-Reactive Immunoconjugates
      Siegall, C.B.,Gawlak, S.L.,Chace, D.,Wolff, E.A.,Mixan, B.,Marquardt, H.
      (1994) Bioconjug.Chem. 5: 423


    Organizational Affiliation

    Molecular Immunology Department, Bristol-Myers Squibb Pharmaceutical Research Institute, Seattle, Washington 98121, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BRYODIN I
Y, Z
248Bryonia dioicaEC: 3.2.2.22
Find proteins for P33185 (Bryonia dioica)
Go to UniProtKB:  P33185
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.720α = 90.00
b = 77.563β = 90.00
c = 115.601γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
DENZOdata reduction
X-PLORphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-03-04
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance