1vai

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1vai, resolution 1.80Å ()
Non-Standard Residues: ,
Activity: Peptidylprolyl isomerase, with EC number 5.2.1.8
Related: 1v9t, 1j2a
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml



Contents

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

Publication Abstract from PubMed

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.

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, Eur J Biochem. 2004 Sep;271(18):3794-803. PMID:15355356

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

1vai is a 3 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA.

See Also

Reference

  • Konno M, Sano Y, Okudaira K, Kawaguchi Y, Yamagishi-Ohmori Y, Fushinobu S, Matsuzawa H. Escherichia coli cyclophilin B binds a highly distorted form of trans-prolyl peptide isomer. Eur J Biochem. 2004 Sep;271(18):3794-803. PMID:15355356 doi:10.1111/j.1432-1033.2004.04321.x

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