PDBsum entry 1h0p

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Isomerase PDB id
Protein chain
182 a.a. *
Waters ×201
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Cyclophilin_5 from c. Elegans
Structure: Peptidyl-prolyl cis-trans isomerase 5. Chain: a. Fragment: residues 23-204. Synonym: ppiase, rotamase, cyclophilin-5. Engineered: yes. Mutation: yes
Source: Caenorhabditis elegans. Organism_taxid: 6239. Expressed in: escherichia coli. Expression_system_taxid: 469008.
1.75Å     R-factor:   0.180     R-free:   0.250
Authors: N.C.Picken,S.Eschenlauer,P.Taylor,A.P.Page,M.D.Walkinshaw
Key ref:
N.C.Picken et al. (2002). Structural and biological characterisation of the gut-associated cyclophilin B isoforms from Caenorhabditis elegans. J Mol Biol, 322, 15-25. PubMed id: 12215411 DOI: 10.1016/S0022-2836(02)00712-X
26-Jun-02     Release date:   12-Sep-02    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P52013  (CYP5_CAEEL) -  Peptidyl-prolyl cis-trans isomerase 5
204 a.a.
182 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     cytoplasm   1 term 
  Biological process     protein folding   2 terms 
  Biochemical function     isomerase activity     2 terms  


    Added reference    
DOI no: 10.1016/S0022-2836(02)00712-X J Mol Biol 322:15-25 (2002)
PubMed id: 12215411  
Structural and biological characterisation of the gut-associated cyclophilin B isoforms from Caenorhabditis elegans.
N.C.Picken, S.Eschenlauer, P.Taylor, A.P.Page, M.D.Walkinshaw.
The free-living nematode Caenorhabditis elegans expresses 18 cyclophilin isoforms, eight of which are conserved single domain forms, comprising two closely related secreted or type B forms (CYP-5 and CYP-6). Recombinant CYP-5 has been purified, crystallised and the X-ray structure solved to a resolution of 1.75A. The detailed molecular architecture most strongly resembles the structure of human cyclophilin B with conserved changes in loop structure and N and C-terminal extensions. Interestingly, the active site pocket is occupied by a molecule of dithiothreitol though this has little effect on the geometry of the active site which is similar to other cyclophilin structures. The peptidyl-prolyl isomerase activity of CYP-5 has been characterised against the substrate N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide, and gives a k(cat)/K(m) value of 3.6x10(6)M(-1)s(-1) that compares with a value of 6.3x10(6)M(-1)s(-1) for human cyclophilin B. The immunosuppressive drug cyclosporin A binds and inhibits CYP-5 with an IC(50) value of 50nM, which is comparable to the value of 84nM found for human cyclophilin B. CYP-6 has 67% sequence identity with CYP-5 and a molecular model was built based on the CYP-5 crystal structure. The model shows that CYP-5 and CYP-6 are likely to have very similar structures, but with a markedly increased number of negative charges distributed around the surface of CYP-6. The spatial expression patterns of the cyclophilin B isoforms were examined using transgenic animals carrying a LacZ reporter fusion to these genes, and both cyp-5 and cyp-6 are found to be expressed in an overlapping fashion in the nematode gut. The temporal expression pattern of cyp-5 was further determined and revealed a constitutive expression pattern, with highest abundance levels being found in the embryo.
  Selected figure(s)  
Figure 1.
Figure 1. Sequence alignments. CYP5_STRUCT is the sequence used for structure determination. The first 21 residues were cleaved and the N-terminal of the crystallised protein begins with the sequence KGPKV. This sequence is compared with the database entry for CYP-5 accession number P52013 (CYP5_CAEEL); C. elegans CYP-6 accession number P52014 (CYP6_CAEEL), human CypB (CYPB_HUMAN), C. elegans CYP-3 accession number P52011 (CYP3_CAEEL) and human CypA accession number P05092 (CYPA_HUMAN). The sequences were aligned using CLUSTAL W. N-terminal signal sequences are highlighted in italics, loop regions are shown in bold, active site residues are underlined, those residues involved in the interaction with DTT molecule are in bold and underlined and the shaded residues are those that are not conserved between the CYP-5 and CYP-6 structures.
Figure 2.
Figure 2. Structural comparisons of B-type cyclophilins. (a) Overlay of the structures of C. elegans CYP-5 (shown and labelled in blue) and human CypB (shown in red). Side-chain positions for loop residues E51 and K52 of hCypB and P67 (higlighted) and K68 of CYP-5 are shown. (b) Stereo picture showing DTT bound in the active site of CYP-5. Residues involved in the interaction with DTT, Arg79, Arg149 and His150 are shown in cyan. CsA from the human CypB structure is overlaid (red) to show DTT in a similar binding position. (c) Electrostatic potential surfaces for CYP-5 (left) and CYP-6 (right). The potential at the surface is colour-coded from most positive (violet) through to most negative (red). The crystallographically determined dithiothreitol molecule is shown bound in the active site of CYP-5.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 322, 15-25) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21337480 C.J.Dunsmore, K.J.Malone, K.R.Bailey, M.A.Wear, H.Florance, S.Shirran, P.E.Barran, A.P.Page, M.D.Walkinshaw, and N.J.Turner (2011).
Design and synthesis of conformationally constrained cyclophilin inhibitors showing a cyclosporin-A phenotype in C. elegans.
  Chembiochem, 12, 802-810.  
17922928 J.Búa, L.E.Fichera, A.G.Fuchs, M.Potenza, M.Dubin, R.O.Wenger, G.Moretti, C.M.Scabone, and A.M.Ruiz (2008).
Anti-Trypanosoma cruzi effects of cyclosporin A derivatives: possible role of a P-glycoprotein and parasite cyclophilins.
  Parasitology, 135, 217-228.  
18629211 T.J.Pemberton, and J.E.Kay (2005).
Identification and Comparative Analysis of the Peptidyl-Prolyl cis/trans Isomerase Repertoires of H. sapiens, D. melanogaster, C. elegans, S. cerevisiae and Sz. pombe.
  Comp Funct Genomics, 6, 277-300.  
12424233 S.C.Eschenlauer, and A.P.Page (2003).
The Caenorhabditis elegans ERp60 homolog protein disulfide isomerase-3 has disulfide isomerase and transglutaminase-like cross-linking activity and is involved in the maintenance of body morphology.
  J Biol Chem, 278, 4227-4237.  
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