6HMZ

Crystal Structure of a Single-Domain Cyclophilin from Brassica napus Phloem Sap


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Enzyme activity and structural features of three single-domain phloem cyclophilins from Brassica napus.

Hanhart, P.Falke, S.Garbe, M.Rose, V.Thiess, M.Betzel, C.Kehr, J.

(2019) Sci Rep 9: 9368-9368

  • DOI: 10.1038/s41598-019-45856-y

  • PubMed Abstract: 
  • Cyclophilins (CYPs) are a group of ubiquitous prolyl cis/trans isomerases (PPIases). It was shown that plants possess the most diverse CYP families and that these are abundant in the phloem long-distance translocation stream. Since phloem exudate sho ...

    Cyclophilins (CYPs) are a group of ubiquitous prolyl cis/trans isomerases (PPIases). It was shown that plants possess the most diverse CYP families and that these are abundant in the phloem long-distance translocation stream. Since phloem exudate showed PPIase activity, three single-domain CYPs that occur in phloem samples from Brassica napus were characterised on functional and structural levels. It could be shown that they exhibit isomerase activity and that this activity is controlled by a redox regulation mechanism, which has been postulated for divergent CYPs. The structure determination by small-angle X-ray scattering experiments revealed a conserved globular shape. In addition, the high-resolution crystal structure of BnCYP19-1 was resolved and refined to 2.0 Å resolution, and the active sites of related CYPs as well as substrate binding were modelled. The obtained data and results support the hypothesis that single domain phloem CYPs are active phloem PPIases that may function as chaperones.


    Organizational Affiliation

    Universität Hamburg, Institute of Plant Science and Microbiology, Molecular Plant Genetics, Ohnhorststraße 18, 22609, Hamburg, Germany. julia.kehr@uni-hamburg.de.,Universität Hamburg, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Notkestraße 85, 22603, Hamburg, Germany.,Universität Hamburg, Institute of Plant Science and Microbiology, Molecular Plant Genetics, Ohnhorststraße 18, 22609, Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase
X
180Brassica napusMutation(s): 0 
Gene Names: BnaA09g35540D
EC: 5.2.1.8
Find proteins for A0A078GRH6 (Brassica napus)
Go to UniProtKB:  A0A078GRH6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cyclosporin
A
11N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLI
Query on MLI

Download SDF File 
Download CCD File 
X
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
X
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  6 Unique
IDChainsTypeFormula2D DiagramParent
ABA
Query on ABA
A
L-PEPTIDE LINKINGC4 H9 N O2ALA
SAR
Query on SAR
A
PEPTIDE LINKINGC3 H7 N O2GLY
MLE
Query on MLE
A
L-PEPTIDE LINKINGC7 H15 N O2LEU
DAL
Query on DAL
A
D-PEPTIDE LINKINGC3 H7 N O2

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BMT
Query on BMT
A
L-PEPTIDE LINKINGC10 H19 N O3THR
MVA
Query on MVA
A
L-PEPTIDE LINKINGC6 H13 N O2VAL
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 86.580α = 90.00
b = 86.580β = 90.00
c = 119.520γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
iMOSFLMdata reduction
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionGermanyPCIG14-GA-2013-63 0734
GermanyLFF-GK06 (DELIGRAH)
German Research FoundationGermanyDFG KE 856_6-1

Revision History 

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2019-07-10
    Type: Data collection, Database references