PDBsum entry 1vai

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Isomerase PDB id
Protein chains
166 a.a. *
Waters ×197
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Structure of e. Coli cyclophilin b k163t mutant bound to n- acetyl-ala-ala-pro-ala-7-amino-4-methylcoumarin
Structure: Cyclophilin b. Chain: a, b. Synonym: ppiase a, rotamase a, cyclophilin a. Engineered: yes. Mutation: yes. (Ace)aapa(mcm). Chain: c. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: chemically synthesized
1.80Å     R-factor:   0.188     R-free:   0.229
Authors: M.Konno,Y.Sano,K.Okudaira,Y.Kawaguchi,Y.Yamagishi-Ohmori, S.Fushinobu,H.Matsuzawa
Key ref:
M.Konno et al. (2004). Escherichia coli cyclophilin B binds a highly distorted form of trans-prolyl peptide isomer. Eur J Biochem, 271, 3794-3803. PubMed id: 15355356 DOI: 10.1111/j.1432-1033.2004.04321.x
17-Feb-04     Release date:   21-Sep-04    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P0AFL3  (PPIA_ECOLI) -  Peptidyl-prolyl cis-trans isomerase A
190 a.a.
166 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Peptidylprolyl isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Peptidylproline (omega=180) = peptidylproline (omega=0)
Peptidylproline (omega=180)
= peptidylproline (omega=0)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     periplasmic space   2 terms 
  Biological process     protein folding   2 terms 
  Biochemical function     isomerase activity     2 terms  


    Added reference    
DOI no: 10.1111/j.1432-1033.2004.04321.x Eur J Biochem 271:3794-3803 (2004)
PubMed id: 15355356  
Escherichia coli cyclophilin B binds a highly distorted form of trans-prolyl peptide isomer.
M.Konno, Y.Sano, K.Okudaira, Y.Kawaguchi, Y.Yamagishi-Ohmori, S.Fushinobu, H.Matsuzawa.
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.
  Selected figure(s)  
Figure 2.
Fig. 2. The ribbon model of the -barrel structure of E. coli CyPB consisting of the upper and the lower -sheets enclosed by two helices. The colors of ribbon are shown corresponding to those of Fig. 1. The loop colored in green is the region expected to affect the selection of the substrate. Thr163 is located outside of 8 strand. The Suc-Ala-trans-Pro-Ala-pNA is also shown by ball-and-sticks model. Figures 2,3,4,5,6 and 7 were prepared using the programs MOLSCRIPT[35] and RASTER3D[36].
Figure 4.
Fig. 4. A stereo view of Suc-Ala-trans-Pro-Ala-pNA (green) and Ac-Ala-Ala-trans-Pro-Ala-AMC (yellow) bound to superimposed E. coli CyPB molecules. The hydrogen bonds are shown in broken lines. The CyPB molecules shown in Figs 4, 6 and 7 were rotated by 45° around the horizontal axis from those shown in Figs 2 and 3.
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: Eur J Biochem (2004, 271, 3794-3803) copyright 2004.  
  Figures were selected by the author.  
    Author's comment    
  The tripeptide Suc-Ala-Pro-Ala-pNA and the tetrapeptide Ac-Ala-Ala-Pro-Ala-AMC have the distorted trans-form, allowing them to bury deeply into the cleft of CyPB molecules. The Ala-Pro-Ala segments of the tripeptide and tetrapeptide occupy the exactly same positions. The phi and psi angles of the Ala residue of Ala-Pro are rarely observed for residues of linear short peptides containing no glycine.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
16544291 K.K.Jin, S.S.Krishna, R.Schwarzenbacher, D.McMullan, P.Abdubek, S.Agarwalla, E.Ambing, H.Axelrod, J.M.Canaves, H.J.Chiu, A.M.Deacon, M.DiDonato, M.A.Elsliger, J.Feuerhelm, A.Godzik, C.Grittini, S.K.Grzechnik, J.Hale, E.Hampton, J.Haugen, M.Hornsby, L.Jaroszewski, H.E.Klock, M.W.Knuth, E.Koesema, A.Kreusch, P.Kuhn, S.A.Lesley, M.D.Miller, K.Moy, E.Nigoghossian, L.Okach, S.Oommachen, J.Paulsen, K.Quijano, R.Reyes, C.Rife, R.C.Stevens, G.Spraggon, H.van den Bedem, J.Velasquez, A.White, G.Wolf, G.W.Han, Q.Xu, K.O.Hodgson, J.Wooley, and I.A.Wilson (2006).
Crystal structure of TM1367 from Thermotoga maritima at 1.90 A resolution reveals an atypical member of the cyclophilin (peptidylprolyl isomerase) fold.
  Proteins, 63, 1112-1118.
PDB code: 1zx8
15978068 J.E.Mogensen, and D.E.Otzen (2005).
Interactions between folding factors and bacterial outer membrane proteins.
  Mol Microbiol, 57, 326-346.  
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