PDBsum entry 1clh

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Isomerase(peptidyl-prolyl cis-trans) PDB id
Protein chain
166 a.a. *
* Residue conservation analysis
PDB id:
Name: Isomerase(peptidyl-prolyl cis-trans)
Title: Three-dimensional solution structure of escherichia coli periplasmic cyclophilin
Structure: Cyclophilin. Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: cyclophilin.
NMR struc: 12 models
Authors: R.T.Clubb,G.Wagner
Key ref:
R.T.Clubb et al. (1994). Three-dimensional solution structure of Escherichia coli periplasmic cyclophilin. Biochemistry, 33, 2761-2772. PubMed id: 8130188 DOI: 10.1021/bi00176a004
20-Dec-93     Release date:   31-May-94    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P0AFL3  (PPIA_ECOLI) -  Peptidyl-prolyl cis-trans isomerase A
190 a.a.
166 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     protein folding   2 terms 
  Biochemical function     isomerase activity     2 terms  


    Added reference    
DOI no: 10.1021/bi00176a004 Biochemistry 33:2761-2772 (1994)
PubMed id: 8130188  
Three-dimensional solution structure of Escherichia coli periplasmic cyclophilin.
R.T.Clubb, S.B.Ferguson, C.T.Walsh, G.Wagner.
The solution structure of the periplasmic cyclophilin type cis-trans peptidyl-prolyl isomerase from Escherichia coli (167 residues, MW > 18.200) has been determined using multidimensional heteronuclear NMR spectroscopy and distance geometry calculations. The structure determination is based on a total of 1720 NMR-derived restraints (1566 distance and 101 phi and 53 chi 1 torsion angle restraints). Twelve distance geometry structures were calculated, and the average root-mean-square (rms) deviation about the mean backbone coordinate positions is 0.84 +/- 0.18 A for the backbone atoms of residues 5-165 of the ensemble. The three-dimensional structure of E. coli cyclophilin consists of an eight-stranded antiparallel beta-sheet barrel capped by alpha-helices. The average coordinates of the backbone atoms of the core residues of E. coli cyclophilin have an rms deviation of 1.44 A, with conserved regions in the crystal structure of unligated human T cell cyclophilin [Ke, H. (1992) J. Mol. Biol. 228, 539-550]. Four regions proximal to the active site differ substantially and may determine protein substrate specificity, sensitivity to cyclosporin A, and the composite drug:protein surface required to inhibit calcineurin. A residue essential for isomerase activity in human T cell cyclophilin (His126) is replaced by Tyr122 in E. coli cyclophilin without affecting enzymatic activity.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21234551 E.A.Kapellios, S.Karamanou, M.F.Sardis, M.Aivaliotis, A.Economou, and S.A.Pergantis (2011).
Using nanoelectrospray ion mobility spectrometry (GEMMA) to determine the size and relative molecular mass of proteins and protein assemblies: a comparison with MALLS and QELS.
  Anal Bioanal Chem, 399, 2421-2433.  
20486767 E.S.Lovelace, S.Gunasekera, C.Alvarmo, R.J.Clark, S.T.Nevin, A.A.Grishin, D.J.Adams, D.J.Craik, and N.L.Daly (2011).
Stabilization of α-conotoxin AuIB: influences of disulfide connectivity and backbone cyclization.
  Antioxid Redox Signal, 14, 87-95.  
17225137 P.Mark, and L.Nilsson (2007).
A molecular dynamics study of Cyclophilin A free and in complex with the Ala-Pro dipeptide.
  Eur Biophys J, 36, 213-224.  
17103061 A.Manteca, A.I.Pelaez, R.Zardoya, and J.Sanchez (2006).
Actinobacteria cyclophilins: phylogenetic relationships and description of new class- and order-specific paralogues.
  J Mol Evol, 63, 719-732.  
15978068 J.E.Mogensen, and D.E.Otzen (2005).
Interactions between folding factors and bacterial outer membrane proteins.
  Mol Microbiol, 57, 326-346.  
16176267 T.Murata, H.Hemmi, S.Nakamura, K.Shimizu, Y.Suzuki, and I.Yamaguchi (2005).
Structure, epitope mapping, and docking simulation of a gibberellin mimic peptide as a peptidyl mimotope for a hydrophobic ligand.
  FEBS J, 272, 4938-4948.
PDB code: 1yt6
15123712 A.Mayasundari, N.A.Whittemore, E.H.Serpersu, and C.B.Peterson (2004).
The solution structure of the N-terminal domain of human vitronectin: proximal sites that regulate fibrinolysis and cell migration.
  J Biol Chem, 279, 29359-29366.
PDB code: 1s4g
15173163 N.A.Horn, G.B.Hurst, A.Mayasundari, N.A.Whittemore, E.H.Serpersu, and C.B.Peterson (2004).
Assignment of the four disulfides in the N-terminal somatomedin B domain of native vitronectin isolated from human plasma.
  J Biol Chem, 279, 35867-35878.  
15023339 S.L.Rowland, W.F.Burkholder, K.A.Cunningham, M.W.Maciejewski, A.D.Grossman, and G.F.King (2004).
Structure and mechanism of action of Sda, an inhibitor of the histidine kinases that regulate initiation of sporulation in Bacillus subtilis.
  Mol Cell, 13, 689-701.
PDB code: 1pv0
12676931 H.Hemmi, J.Ishibashi, T.Tomie, and M.Yamakawa (2003).
Structural basis for new pattern of conserved amino acid residues related to chitin-binding in the antifungal peptide from the coconut rhinoceros beetle Oryctes rhinoceros.
  J Biol Chem, 278, 22820-22827.
PDB code: 1iyc
14991679 J.Ying, K.E.Kövér, X.Gu, G.Han, D.B.Trivedi, M.J.Kavarana, and V.J.Hruby (2003).
Solution structures of cyclic melanocortin agonists and antagonists by NMR.
  Biopolymers, 71, 696-716.  
12186551 H.Hemmi, T.Yoshida, T.Kumazaki, N.Nemoto, J.Hasegawa, F.Nishioka, Y.Kyogoku, H.Yokosawa, and Y.Kobayashi (2002).
Solution structure of ascidian trypsin inhibitor determined by nuclear magnetic resonance spectroscopy.
  Biochemistry, 41, 10657-10664.
PDB code: 1iw4
11297417 H.Hemmi, J.M.Studts, Y.K.Chae, J.Song, J.L.Markley, and B.G.Fox (2001).
Solution structure of the toluene 4-monooxygenase effector protein (T4moD).
  Biochemistry, 40, 3512-3524.
PDB codes: 1g10 1g11
11294627 K.J.Rosengren, N.L.Daly, M.J.Scanlon, and D.J.Craik (2001).
Solution structure of BSTI: a new trypsin inhibitor from skin secretions of Bombina bombina.
  Biochemistry, 40, 4601-4609.
PDB code: 1hx2
11358512 W.Shao, E.Fernandez, A.Sachpatzidis, J.Wilken, D.A.Thompson, B.I.Schweitzer, and E.Lolis (2001).
CCR2 and CCR5 receptor-binding properties of herpesvirus-8 vMIP-II based on sequence analysis and its solution structure.
  Eur J Biochem, 268, 2948-2959.
PDB code: 1hhv
11123900 A.M.McManus, N.F.Dawson, J.D.Wade, L.E.Carrington, D.J.Winzor, and D.J.Craik (2000).
Three-dimensional structure of RK-1: a novel alpha-defensin peptide.
  Biochemistry, 39, 15757-15764.
PDB code: 1ews
10903497 J.M.Hill, P.F.Alewood, and D.J.Craik (2000).
Conotoxin TVIIA, a novel peptide from the venom of Conus tulipa 2. Three-dimensional solution structure.
  Eur J Biochem, 267, 4649-4657.
PDB code: 1eyo
10913244 K.L.Mayer, and M.J.Stone (2000).
NMR solution structure and receptor peptide binding of the CC chemokine eotaxin-2.
  Biochemistry, 39, 8382-8395.
PDB codes: 1eig 1eih
11058892 M.T.Ivery (2000).
Immunophilins: switched on protein binding domains?
  Med Res Rev, 20, 452-484.  
10713041 U.Reidt, K.Reuter, T.Achsel, D.Ingelfinger, R.Lührmann, and R.Ficner (2000).
Crystal structure of the human U4/U6 small nuclear ribonucleoprotein particle-specific SnuCyp-20, a nuclear cyclophilin.
  J Biol Chem, 275, 7439-7442.
PDB code: 1qoi
9988686 E.Dirnbach, D.G.Steel, and A.Gafni (1999).
Proline isomerization is unlikely to be the cause of slow annealing and reactivation during the folding of alkaline phosphatase.
  J Biol Chem, 274, 4532-4536.  
10320325 H.Sticht, S.E.Escher, K.Schweimer, W.G.Forssmann, P.Rösch, and K.Adermann (1999).
Solution structure of the human CC chemokine 2: A monomeric representative of the CC chemokine subtype.
  Biochemistry, 38, 5995-6002.
PDB code: 2hcc
9931005 L.S.Mizoue, J.F.Bazan, E.C.Johnson, and T.M.Handel (1999).
Solution structure and dynamics of the CX3C chemokine domain of fractalkine and its interaction with an N-terminal fragment of CX3CR1.
  Biochemistry, 38, 1402-1414.
PDB code: 1b2t
  9655334 V.Mikol, D.Ma, and C.K.Carlow (1998).
Crystal structure of the cyclophilin-like domain from the parasitic nematode Brugia malayi.
  Protein Sci, 7, 1310-1316.
PDB code: 1a33
9634701 W.J.Fairbrother, M.A.Champe, H.W.Christinger, B.A.Keyt, and M.A.Starovasnik (1998).
Solution structure of the heparin-binding domain of vascular endothelial growth factor.
  Structure, 6, 637-648.
PDB codes: 1vgh 2vgh
9622482 W.Shao, L.F.Jerva, J.West, E.Lolis, and B.I.Schweitzer (1998).
Solution structure of murine macrophage inflammatory protein-2.
  Biochemistry, 37, 8303-8313.
PDB code: 1mi2
9384567 J.I.Fletcher, B.E.Chapman, J.P.Mackay, M.E.Howden, and G.F.King (1997).
The structure of versutoxin (delta-atracotoxin-Hv1) provides insights into the binding of site 3 neurotoxins to the voltage-gated sodium channel.
  Structure, 5, 1525-1535.
PDB code: 1vtx
9228949 J.I.Fletcher, R.Smith, S.I.O'Donoghue, M.Nilges, M.Connor, M.E.Howden, M.J.Christie, and G.F.King (1997).
The structure of a novel insecticidal neurotoxin, omega-atracotoxin-HV1, from the venom of an Australian funnel web spider.
  Nat Struct Biol, 4, 559-566.
PDB code: 1axh
9294166 M.A.Starovasnik, A.C.Braisted, and J.A.Wells (1997).
Structural mimicry of a native protein by a minimized binding domain.
  Proc Natl Acad Sci U S A, 94, 10080-10085.
PDB codes: 1zda 1zdb 1zdc 1zdd
18642336 M.Moutiez, R.Guthapfel, P.Gueguen, and E.Quéméneur (1997).
New formulae for folding catalysts make them multi-purpose enzymes.
  Biotechnol Bioeng, 56, 645-649.  
  9286985 Y.R.Thorstenson, Y.Zhang, P.S.Olson, and D.Mascarenhas (1997).
Leaderless polypeptides efficiently extracted from whole cells by osmotic shock.
  J Bacteriol, 179, 5333-5339.  
8612612 A.Galat (1996).
A note on circular-dichroic-constrained prediction of protein secondary structure.
  Eur J Biochem, 236, 428-435.  
8639490 N.E.Jacobsen, N.Abadi, M.X.Sliwkowski, D.Reilly, N.J.Skelton, and W.J.Fairbrother (1996).
High-resolution solution structure of the EGF-like domain of heregulin-alpha.
  Biochemistry, 35, 3402-3417.
PDB codes: 1hae 1haf
8639605 T.M.Handel, and P.J.Domaille (1996).
Heteronuclear (1H, 13C, 15N) NMR assignments and solution structure of the monocyte chemoattractant protein-1 (MCP-1) dimer.
  Biochemistry, 35, 6569-6584.
PDB codes: 1dom 1don
  8528067 D.P.Meininger, M.J.Hunter, and E.A.Komives (1995).
Synthesis, activity, and preliminary structure of the fourth EGF-like domain of thrombomodulin.
  Protein Sci, 4, 1683-1695.
PDB code: 1zaq
7673124 M.E.Cardenas, E.Lim, and J.Heitman (1995).
Mutations that perturb cyclophilin A ligand binding pocket confer cyclosporin A resistance in Saccharomyces cerevisiae.
  J Biol Chem, 270, 20997-21002.  
  8580839 S.R.Van Doren, A.V.Kurochkin, W.Hu, Q.Z.Ye, L.L.Johnson, D.J.Hupe, and E.R.Zuiderweg (1995).
Solution structure of the catalytic domain of human stromelysin complexed with a hydrophobic inhibitor.
  Protein Sci, 4, 2487-2498.
PDB codes: 1ums 1umt
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