1V9T

Structure of E. coli cyclophilin B K163T mutant bound to succinyl-ALA-PRO-ALA-P-nitroanilide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Escherichia coli cyclophilin B binds a highly distorted form of trans-prolyl peptide isomer

Konno, M.Sano, Y.Okudaira, K.Kawaguchi, Y.Yamagishi-Ohmori, Y.Fushinobu, S.Matsuzawa, H.

(2004) Eur.J.Biochem. 271: 3794-3803

  • DOI: 10.1111/j.1432-1033.2004.04321.x
  • Primary Citation of Related Structures:  1J2A, 1VAI

  • PubMed Abstract: 
  • Cyclophilins facilitate the peptidyl-prolyl isomerization of a trans-isomer to a cis-isomer in the refolding process of unfolded proteins to recover the natural folding state with cis-proline conformation. To date, only short peptides with a cis-form ...

    Cyclophilins facilitate the peptidyl-prolyl isomerization of a trans-isomer to a cis-isomer in the refolding process of unfolded proteins to recover the natural folding state with cis-proline conformation. To date, only short peptides with a cis-form proline have been observed in complexes of human and Escherichia coli proteins of cyclophilin A, which is present in cytoplasm. The crystal structures analyzed in this study show two complexes in which peptides having a trans-form proline, i.e. succinyl-Ala-trans-Pro-Ala-p-nitroanilide and acetyl-Ala-Ala-trans-Pro-Ala-amidomethylcoumarin, are bound on a K163T mutant of Escherichia coli cyclophilin B, the preprotein of which has a signal sequence. Comparison with cis-form peptides bound to cyclophilin A reveals that in any case the proline ring is inserted into the hydrophobic pocket and a hydrogen bond between CO of Pro and Neta2 of Arg is formed to fix the peptide. On the other hand, in the cis-isomer, the formation of two hydrogen bonds of NH and CO of Ala preceding Pro with the protein fixes the peptide, whereas in the trans-isomer formation of a hydrogen bond between CO preceding Ala-Pro and His47 Nepsilon2 via a mediating water molecule allows the large distortion in the orientation of Ala of Ala-Pro. Although loss of double bond character of the amide bond of Ala-Pro is essential to the isomerization pathway occurring by rotating around its bond, these peptides have forms impossible to undergo proton transfer from the guanidyl group of Arg to the prolyl N atom, which induces loss of double bond character.


    Organizational Affiliation

    Department of Chemistry, Ochanomizu University, Otsuka, Bunkyo-ku, Tokyo, Japan. konno@cc.ocha.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cyclophilin B
A, B
166Escherichia coli (strain K12)Gene Names: ppiA (rot, rotA)
EC: 5.2.1.8
Find proteins for P0AFL3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AFL3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
(SIN)APA(NIT)
C
5N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000400
Query on PRD_000400
CSUCCINYL-ALA-PRO-ALA-P-NITROANILIDEPeptide-like / Inhibitor

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.184 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 79.280α = 90.00
b = 79.280β = 90.00
c = 56.630γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-09-05
    Type: Derived calculations
  • Version 1.4: 2012-12-12
    Type: Other