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1V9T

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

Summary for 1V9T
Entry DOI10.2210/pdb1v9t/pdb
Related1J2A
Related PRD IDPRD_000400
Descriptorcyclophilin B, (SIN)APA(NIT) (3 entities in total)
Functional Keywordsbeta barrel, isomerase-isomerase inhibitor complex, isomerase/isomerase inhibitor
Biological sourceEscherichia coli
More
Total number of polymer chains3
Total formula weight36618.12
Authors
Konno, M.,Sano, Y.,Okudaira, K.,Kawaguchi, Y.,Yamagishi-Ohmori, Y.,Fushinobu, S.,Matsuzawa, H. (deposition date: 2004-02-03, release date: 2004-09-21, Last modification date: 2023-10-25)
Primary citationKonno, 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., 271:3794-3803, 2004
Cited by
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.
PubMed: 15355356
DOI: 10.1111/j.1432-1033.2004.04321.x
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (1.7 Å)
Structure validation

226707

數據於2024-10-30公開中

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