Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 18.58 kDa 
• Atom Count: 1548 
• Modelled Residue Count: 172 
• Deposited Residue Count: 173 
• Unique protein chains: 1

1DYW

Biochemical and structural characterization of a divergent loop cyclophilin from Caenorhabditis elegans

• PDB DOI: 10.2210/pdb1DYW/pdb

• Classification: ISOMERASE(PEPTIDYL-PROLYL CIS-TRANS)
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-02-10 Released: 2000-06-22 
• Deposition Author(s): Dornan, J., Page, A.P., Taylor, P., Wu, S.Y., Winter, A.D., Husi, H., Walkinshaw, M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.286 
• R-Value Observed: 0.215 

Literature

Biochemical and Structural Characterization of a Divergent Loop Cyclophilin from Caenorhabditis Elegans

Dornan, J., Page, A.P., Taylor, P., Wu, S.Y., Winter, A.D., Husi, H., Walkinshaw, M.D.

(1999) J Biol Chem 274: 34877

• PubMed: 10574961 
• DOI: 10.1074/jbc.274.49.34877
• Primary Citation of Related Structures:  
  1DYW


• PubMed Abstract: 
  

Cyclophilin 3 (CYP-3) is one of the most abundantly expressed cyclophilin isoforms in the free living nematode Caenorhabditis elegans. The detailed post-embryonic expression pattern of the cyp-3 transcript is unusual, peaking during early larval development. The spatial expression pattern was examined via reporter gene analysis demonstrating that the cyp-3 transcript is exclusively expressed in the single anterior excretory cell. Recombinant cyclophilin 3 has been purified, crystallized and solved to a resolution of 1.8 A. The peptidyl-prolyl isomerase activity of CYP-3 has been characterized against the substrate N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide, and gives a k(cat)/K(m) value of 2.4 x 10(6) M(-1) s(-1). The immunosuppressive drug cyclosporin A binds and inhibits CYP-3 with an IC(50) value of 16 nM, comparable with the range of values found for human cyclophilin A. The x-ray structure shows that the overall fold and active site geometry is similar to other cyclophilin structures. There are however a number of distinctive features, and we use this structure and amino acid sequence alignment analysis to identify a subgroup of "divergent-loop cyclophilins". This subgroup has a number of uniquely conserved features: an additional loop between residues 48 and 54 (KSGKPLH); two cysteine residues (Cys(40) and Cys(168)) that are in close proximity but remain in the unoxidized form, and two other conserved residues, His(54) and Glu(83). We suggest that these features are functionally important for the role played by this class of cyclophilins during cellular responses to stress caused by changes in the redox environment or by up-regulation of cellular activity. This study represents a detailed biological, biochemical, and structural characterization of a single cyclophilin isoform in the model organism Caenorhabditis elegans.

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Related Citations: 

• X-Ray Structure of a Monomeric Cyclophilin
  Mikol, V., Kallen, J., Pfluegl, G., Walkinshaw, M.D.
  (1993) J Mol Biol 234: 1119

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Organizational Affiliation: 

Structural Biochemistry Group, Institute of Cell and Molecular Biology, The University of Edinburgh, Michael Swann Building, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLOPHILIN 3	A	173	Caenorhabditis elegans	Mutation(s): 0  Gene Names: cyn-3, cyp-3, Y75B12B.5 EC: 5.2.1.8
UniProt
Find proteins for P52011 (Caenorhabditis elegans) Explore P52011  Go to UniProtKB:  P52011

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.286 
• R-Value Observed: 0.215 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.608	α = 90
b = 60.608	β = 90
c = 123.124	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-02-10 
• Released Date: 2000-06-22 
Deposition Author(s): Dornan, J., Page, A.P., Taylor, P., Wu, S.Y., Winter, A.D., Husi, H., Walkinshaw, M.D.

Revision History  

• Version 1.0: 2000-06-22
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2017-07-05
  Changes: Advisory, Atomic model, Data collection, Derived calculations
• Version 2.1: 2019-05-22
  Changes: Data collection, Refinement description