6HMZ | pdb_00006hmz

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

• PDB DOI: https://doi.org/10.2210/pdb6HMZ/pdb

• Classification: ISOMERASE
• Organism(s): Brassica napus, Tolypocladium inflatum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-09-13 Released: 2018-11-21 
• Deposition Author(s): Falke, S., Hanhart, P., Garbe, M., Thiess, M., Betzel, C., Kehr, J.
• Funding Organization(s): European Commission, German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.223 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

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

• PubMed: 31249367 
• DOI: https://doi.org/10.1038/s41598-019-45856-y
• Primary Citation Related Structures: 
  6HMZ


• 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 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.

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Organizational Affiliation: 
• Universität Hamburg, Institute of Plant Science and Microbiology, Molecular Plant Genetics, Ohnhorststraße 18, 22609, Hamburg, Germany.
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. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, light scattering, SAXS

Macromolecule Content 

• Total Structure Weight: 20.72 kDa 
• Atom Count: 1,422 
• Modeled Residue Count: 181 
• Deposited Residue Count: 191 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase	A [auth X]	180	Brassica napus	Mutation(s): 0  Gene Names: BnaA09g35540D, GSBRNA2T00037123001 EC: 5.2.1.8
UniProt
Find proteins for A0A078GRH6 (Brassica napus) Explore A0A078GRH6  Go to UniProtKB:  A0A078GRH6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclosporin	B [auth A]	11	Tolypocladium inflatum	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	D [auth X]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
MG	C [auth X]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA	B [auth A]	L-PEPTIDE LINKING	C4 H9 N O2		ALA
BMT	B [auth A]	L-PEPTIDE LINKING	C10 H19 N O3		THR
DAL	B [auth A]	D-PEPTIDE LINKING	C3 H7 N O2		--
MLE	B [auth A]	L-PEPTIDE LINKING	C7 H15 N O2		LEU
MVA	B [auth A]	L-PEPTIDE LINKING	C6 H13 N O2		VAL
SAR	B [auth A]	PEPTIDE LINKING	C3 H7 N O2		GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.223 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.58	α = 90
b = 86.58	β = 90
c = 119.52	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-11-21 
Deposition Author(s): Falke, S., Hanhart, P., Garbe, M., Thiess, M., Betzel, C., Kehr, J.

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Funding Organization	Location	Grant Number
European Commission	Germany	PCIG14-GA-2013-63 0734
	Germany	LFF-GK06 (DELIGRAH)
German Research Foundation	Germany	DFG KE 856_6-1

Revision History  

• Version 1.0: 2018-11-21
  Type: Initial release
  
• Version 1.1: 2019-07-10
  Changes: Data collection, Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description