PDBsum entry 1jnt

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Isomerase PDB id
Protein chain
92 a.a. *
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Nmr structure of the e. Coli peptidyl-prolyl cis/trans- isomerase parvulin 10
Structure: Peptidyl-prolyl cis-trans isomerasE C. Chain: a. Synonym: parvulin, ppiasE C, rotamasE C. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: para. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 1 models
Authors: A.Kuehlewein,G.Voll,B.Schelbert,H.Kessler,G.Fischer, J.U.Rahfeld,G.Gemmecker
Key ref:
A.Kühlewein et al. (2004). Solution structure of Escherichia coli Par10: The prototypic member of the Parvulin family of peptidyl-prolyl cis/trans isomerases. Protein Sci, 13, 2378-2387. PubMed id: 15322281 DOI: 10.1110/ps.04756704
25-Jul-01     Release date:   17-Jun-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P0A9L5  (PPIC_ECOLI) -  Peptidyl-prolyl cis-trans isomerase C
93 a.a.
92 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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     cytoplasm   1 term 
  Biological process     metabolic process   2 terms 
  Biochemical function     protein binding     3 terms  


    Added reference    
DOI no: 10.1110/ps.04756704 Protein Sci 13:2378-2387 (2004)
PubMed id: 15322281  
Solution structure of Escherichia coli Par10: The prototypic member of the Parvulin family of peptidyl-prolyl cis/trans isomerases.
A.Kühlewein, G.Voll, B.Hernandez Alvarez, H.Kessler, G.Fischer, J.U.Rahfeld, G.Gemmecker.
E. coli Par10 is a peptidyl-prolyl cis/trans isomerase (PPIase) from Escherichia coli catalyzing the isomerization of Xaa-Pro bonds in oligopeptides with a broad substrate specificity. The structure of E. coli Par10 has been determined by multidimensional solution-state NMR spectroscopy based on 1207 conformational constraints (1067 NOE-derived distances, 42 vicinal coupling-constant restraints, 30 hydrogen-bond restraints, and 68 phi/psi restraints derived from the Chemical Shift Index). Simulated-annealing calculations with the program ARIA and subsequent refinement with XPLOR yielded a set of 18 convergent structures with an average backbone RMSD from mean atomic coordinates of 0.50 A within the well-defined secondary structure elements. E. coli Par10 is the smallest known PPIase so far, with a high catalytic efficiency comparable to that of FKBPs and cyclophilins. The secondary structure of E. coli Par10 consists of four helical regions and a four-stranded antiparallel beta-sheet. The N terminus forms a beta-strand, followed by a large stretch comprising three alpha-helices. A loop region containing a short beta-strand separates these helices from a fourth alpha-helix. The C terminus consists of two more beta-strands completing the four-stranded anti-parallel beta-sheet with strand order 2143. Interestingly, the third beta-strand includes a Gly-Pro cis peptide bond. The curved beta-strand forms a hydrophobic binding pocket together with alpha-helix 4, which also contains a number of highly conserved residues. The three-dimensional structure of Par10 closely resembles that of the human proteins hPin1 and hPar14 and the plant protein Pin1At, belonging to the same family of highly homologous proteins.
  Selected figure(s)  
Figure 3.
Figure 3. Topology of E. coli Par10. Filled arrows symbolize experimental H[ ]-H[ ]NOE contacts; open arrows reflect observed H[N]-H[N] NOEs within the -sheet.
Figure 6.
Figure 6. Orientation of the H-bonds in the -sheet and putative substrate binding site of different Parvulins. (A) Arrangement of the G75-P76 cis amide bond in E. coli Par10, compared with the two homologous structures hPin1 and hPar14. In spite of the bulge resulting from the cis peptide bond, the -sheet of E. coli Par10 can form all four H-bonds whereas the structures of hPar14 and hPin1 with trans-Pro are only stabilized by three H-bonds in this region (figure produced with Insight II, MSI Inc.). (B) Comparison of the putative binding pockets of hPar14 (PDB code 1eq3, green residues) and hPin1 (PDB code 1pin; red residues) overlaid on the E. coli Par10 structure (PDB code 1jnt; blue residues, grey backbone). The labeled residues are highly conserved in all parvulins and may be involved in the catalytic activity of these parvulins (figure produced with MOLMOL, version 2k.1; Koradi et al. 1996). (C) Connolly surface of E. coli Par10. Helix 4 (left) and the curved -sheet form a lipophilic gap (brown), enabling a lipophilic oligopeptide substrate to bind (figure produced with the MOLCAD module of the program Sybyl, version 6.3; Tripos AG).
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2004, 13, 2378-2387) copyright 2004.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21138844 ..Jaremko, M.Jaremko, I.Elfaki, J.W.Mueller, A.Ejchart, P.Bayer, and I.Zhukov (2011).
Structure and dynamics of the first archaeal parvulin reveal a new functionally important loop in parvulin-type prolyl isomerases.
  J Biol Chem, 286, 6554-6565.
PDB code: 2rqs
20487272 H.L.Hyyryläinen, B.C.Marciniak, K.Dahncke, M.Pietiäinen, P.Courtin, M.Vitikainen, R.Seppala, A.Otto, D.Becher, M.P.Chapot-Chartier, O.P.Kuipers, and V.P.Kontinen (2010).
Penicillin-binding protein folding is dependent on the PrsA peptidyl-prolyl cis-trans isomerase in Bacillus subtilis.
  Mol Microbiol, 77, 108-127.  
  19866485 U.Weininger, R.P.Jakob, M.Kovermann, J.Balbach, and F.X.Schmid (2010).
The prolyl isomerase domain of PpiD from Escherichia coli shows a parvulin fold but is devoid of catalytic activity.
  Protein Sci, 19, 6.
PDB code: 2kgj
19309529 O.Heikkinen, R.Seppala, H.Tossavainen, S.Heikkinen, H.Koskela, P.Permi, and I.Kilpeläinen (2009).
Solution structure of the parvulin-type PPIase domain of Staphylococcus aureus PrsA--implications for the catalytic mechanism of parvulins.
  BMC Struct Biol, 9, 17.
PDB code: 2jzv
  19787094 J.W.Mueller, and P.Bayer (2008).
Small family with key contacts: par14 and par17 parvulin proteins, relatives of pin1, now emerge in biomedical research.
  Perspect Medicin Chem, 2, 11-20.  
18509837 N.Wehofsky, C.Wespe, V.Cerovsky, A.Pech, E.Hoess, R.Rudolph, and F.Bordusa (2008).
Ionic liquids and proteases: a clean alliance for semisynthesis.
  Chembiochem, 9, 1493-1499.  
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