5EX2

Crystal structure of cyclophilin AquaCyp293 from Hirschia baltica


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.294 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural and Functional Characterization of a Novel Family of Cyclophilins, the AquaCyps.

Jakob, R.P.Schmidpeter, P.A.Koch, J.R.Schmid, F.X.Maier, T.

(2016) Plos One 11: e0157070-e0157070

  • DOI: 10.1371/journal.pone.0157070
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cyclophilins are ubiquitous cis-trans-prolyl isomerases (PPIases) found in all kingdoms of life. Here, we identify a novel family of cyclophilins, termed AquaCyps, which specifically occurs in marine Alphaproteobacteria, but not in related terrestric ...

    Cyclophilins are ubiquitous cis-trans-prolyl isomerases (PPIases) found in all kingdoms of life. Here, we identify a novel family of cyclophilins, termed AquaCyps, which specifically occurs in marine Alphaproteobacteria, but not in related terrestric species. In addition to a canonical PPIase domain, AquaCyps contain large extensions and insertions. The crystal structures of two representatives from Hirschia baltica, AquaCyp293 and AquaCyp300, reveal the formation of a compact domain, the NIC domain, by the N- and C-terminal extensions together with a central insertion. The NIC domain adopts a novel mixed alpha-helical, beta-sheet fold that is linked to the cyclophilin domain via a conserved disulfide bond. In its overall fold, AquaCyp293 resembles AquaCyp300, but the two proteins utilize distinct sets of active site residues, consistent with differences in their PPIase catalytic properties. While AquaCyp293 is a highly active general PPIase, AquaCyp300 is specific for hydrophobic substrate peptides and exhibits lower overall activity.


    Organizational Affiliation

    Departement Biozentrum, University of Basel, 4056, Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase
A, B
271Hirschia baltica (strain ATCC 49814 / DSM 5838 / IFAM 1418)Mutation(s): 0 
Find proteins for C6XJ17 (Hirschia baltica (strain ATCC 49814 / DSM 5838 / IFAM 1418))
Go to UniProtKB:  C6XJ17
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.294 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 47.940α = 90.00
b = 72.730β = 93.00
c = 73.930γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-11-23 
  • Released Date: 2016-06-22 
  • Deposition Author(s): Jakob, R.P., Maier, T.

Revision History 

  • Version 1.0: 2016-06-22
    Type: Initial release