PDBsum entry 1q6h

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Isomerase PDB id
Protein chains
210 a.a. *
Waters ×468
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Crystal structure of a truncated form of fkpa from escherich
Structure: Fkbp-type peptidyl-prolyl cis-trans isomerase fkp chain: a, b. Synonym: ppiase, rotamase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: fkpa or b3347. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
1.97Å     R-factor:   0.184     R-free:   0.229
Authors: F.A.Saul,J.-P.Arie,B.Vulliez-Le Normand,R.Kahn,J.-M.Betton, G.A.Bentley
Key ref:
F.A.Saul et al. (2004). Structural and functional studies of FkpA from Escherichia coli, a cis/trans peptidyl-prolyl isomerase with chaperone activity. J Mol Biol, 335, 595-608. PubMed id: 14672666 DOI: 10.1016/j.jmb.2003.10.056
13-Aug-03     Release date:   13-Jan-04    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P45523  (FKBA_ECOLI) -  FKBP-type peptidyl-prolyl cis-trans isomerase FkpA
270 a.a.
210 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     periplasmic space   2 terms 
  Biological process     chaperone-mediated protein folding   4 terms 
  Biochemical function     protein binding     4 terms  


    Added reference    
DOI no: 10.1016/j.jmb.2003.10.056 J Mol Biol 335:595-608 (2004)
PubMed id: 14672666  
Structural and functional studies of FkpA from Escherichia coli, a cis/trans peptidyl-prolyl isomerase with chaperone activity.
F.A.Saul, J.P.Arié, B.Vulliez-le Normand, R.Kahn, J.M.Betton, G.A.Bentley.
The protein FkpA from the periplasm of Escherichia coli exhibits both cis/trans peptidyl-prolyl isomerase (PPIase) and chaperone activities. The crystal structure of the protein has been determined in three different forms: as the full-length native molecule, as a truncated form lacking the last 21 residues, and as the same truncated form in complex with the immunosuppressant ligand, FK506. FkpA is a dimeric molecule in which the 245-residue subunit is divided into two domains. The N-terminal domain includes three helices that are interlaced with those of the other subunit to provide all inter-subunit contacts maintaining the dimeric species. The C-terminal domain, which belongs to the FK506-binding protein (FKBP) family, binds the FK506 ligand. The overall form of the dimer is V-shaped, and the different crystal structures reveal a flexibility in the relative orientation of the two C-terminal domains located at the extremities of the V. The deletion mutant FkpNL, comprising the N-terminal domain only, exists in solution as a mixture of monomeric and dimeric species, and exhibits chaperone activity. By contrast, a deletion mutant comprising the C-terminal domain only is monomeric, and although it shows PPIase activity, it is devoid of chaperone function. These results suggest that the chaperone and catalytic activities reside in the N and C-terminal domains, respectively. Accordingly, the observed mobility of the C-terminal domains of the dimeric molecule could effectively adapt these two independent folding functions of FkpA to polypeptide substrates.
  Selected figure(s)  
Figure 1.
Figure 1. Stereo view of the complex formed between FkpA-DCT dimer and the immunosuppressant FK506. Two orthogonal views are shown: (a) perpendicular to, and (b) along, the non-crystallographic 2-fold axis. The structure is shown schematically in ribbon and loop representation. The b strands, present in the C-terminal domains are shown in yellow. Helical regions are coloured green and blue for the respective monomers. The bound FK506 molecules are shown in red.
Figure 3.
Figure 3. Comparison of the C-domain of FkpA-DCT, shown in red, with HuFKBP12, shown in blue, after superposition of equivalent C^a coordinates. The comparison is shown as a stereo view of the C^a skeletons.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 335, 595-608) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20388215 D.S.Ow, D.Y.Lim, P.M.Nissom, A.Camattari, and V.V.Wong (2010).
Co-expression of Skp and FkpA chaperones improves cell viability and alters the global expression of stress response genes during scFvD1.3 production.
  Microb Cell Fact, 9, 22.  
19558490 C.Budiman, K.Bando, C.Angkawidjaja, Y.Koga, K.Takano, and S.Kanaya (2009).
Engineering of monomeric FK506-binding protein 22 with peptidyl prolyl cis-trans isomerase. Importance of a V-shaped dimeric structure for binding to protein substrate.
  FEBS J, 276, 4091-4101.  
18524934 F.Dumetz, E.Duchaud, S.Claverol, N.Orieux, S.Papillon, D.Lapaillerie, and M.Le Hénaff (2008).
Analysis of the Flavobacterium psychrophilum outer-membrane subproteome and identification of new antigenic targets for vaccine by immunomics.
  Microbiology, 154, 1793-1801.  
18554332 J.Hullmann, S.I.Patzer, C.Römer, K.Hantke, and V.Braun (2008).
Periplasmic chaperone FkpA is essential for imported colicin M toxicity.
  Mol Microbiol, 69, 926-937.  
18165359 M.A.Söderberg, and N.P.Cianciotto (2008).
A Legionella pneumophila peptidyl-prolyl cis-trans isomerase present in culture supernatants is necessary for optimal growth at low temperatures.
  Appl Environ Microbiol, 74, 1634-1638.  
18782764 S.Arredondo, L.Segatori, H.F.Gilbert, and G.Georgiou (2008).
De Novo Design and Evolution of Artificial Disulfide Isomerase Enzymes Analogous to the Bacterial DsbC.
  J Biol Chem, 283, 31469-31476.  
18496685 Y.Xu, D.Lewis, and C.P.Chou (2008).
Effect of folding factors in rescuing unstable heterologous lipase B to enhance its overexpression in the periplasm of Escherichia coli.
  Appl Microbiol Biotechnol, 79, 1035-1044.  
16977620 M.S.Wu, K.L.Pan, and C.P.Chou (2007).
Effect of heat-shock proteins for relieving physiological stress and enhancing the production of penicillin acylase in Escherichia coli.
  Biotechnol Bioeng, 96, 956-966.  
16930150 G.Fischer, and S.Wawra (2006).
Polypeptide binding proteins: what remains to be discovered?
  Mol Microbiol, 61, 1388-1396.  
16926407 S.Debroy, V.Aragon, S.Kurtz, and N.P.Cianciotto (2006).
Legionella pneumophila Mip, a surface-exposed peptidylproline cis-trans-isomerase, promotes the presence of phospholipase C-like activity in culture supernatants.
  Infect Immun, 74, 5152-5160.  
15978068 J.E.Mogensen, and D.E.Otzen (2005).
Interactions between folding factors and bacterial outer membrane proteins.
  Mol Microbiol, 57, 326-346.  
15869639 P.Romano, J.Gray, P.Horton, and S.Luan (2005).
Plant immunophilins: functional versatility beyond protein maturation.
  New Phytol, 166, 753-769.  
16267292 S.S.Justice, D.A.Hunstad, J.R.Harper, A.R.Duguay, J.S.Pinkner, J.Bann, C.Frieden, T.J.Silhavy, and S.J.Hultgren (2005).
Periplasmic peptidyl prolyl cis-trans isomerases are not essential for viability, but SurA is required for pilus biogenesis in Escherichia coli.
  J Bacteriol, 187, 7680-7686.  
15670146 Y.Suzuki, K.Takano, and S.Kanaya (2005).
Stabilities and activities of the N- and C-domains of FKBP22 from a psychrotrophic bacterium overproduced in Escherichia coli.
  FEBS J, 272, 632-642.  
15529165 F.Baneyx, and M.Mujacic (2004).
Recombinant protein folding and misfolding in Escherichia coli.
  Nat Biotechnol, 22, 1399-1408.  
15132751 M.Miot, and J.M.Betton (2004).
Protein quality control in the bacterial periplasm.
  Microb Cell Fact, 3, 4.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.