Structure of e. coli cyclophilin B K163T mutant bound to n-acetyl-ala-ala-pro-ala-7-amino-4-methylcoumarin

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.188 

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This is version 1.5 of the entry. See complete history


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: https://doi.org/10.1111/j.1432-1033.2004.04321.x
  • Primary Citation of Related Structures:  
    1J2A, 1V9T, 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 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cyclophilin B
A, B
166Escherichia coliMutation(s): 1 
Find proteins for P0AFL3 (Escherichia coli (strain K12))
Explore P0AFL3 
Go to UniProtKB:  P0AFL3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFL3
Sequence Annotations
  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
(ACE)AAPA(MCM)6N/AMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.188 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.73α = 90
b = 78.73β = 90
c = 56.16γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-21
    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: 2013-02-27
    Changes: Other
  • Version 1.4: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-10-25
    Changes: Data collection, Refinement description