6HMZ

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.223
R-Value Work: 0.184
R-Value Observed: 0.186

wwPDB Validation 3D Report Full Report

This is version 1.2 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

PubMed: 31249367 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41598-019-45856-y
Primary Citation of 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.

Organizational Affiliation

Universität Hamburg, Institute of Plant Science and Microbiology, Molecular Plant Genetics, Ohnhorststraße 18, 22609, Hamburg, Germany.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A078GRH6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclosporin	B [auth A]	11	Tolypocladium inflatum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLI Query on MLI Download Ideal Coordinates CCD File SDF format, chain D [auth X] MOL2 format, chain D [auth X]	D [auth X]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain D [auth X] Interactions & Density Focus chain D [auth X]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth X] MOL2 format, chain C [auth X]	C [auth X]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth X] Interactions & Density Focus chain C [auth X]

Modified Residues 5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA Query on ABA	B [auth A]	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA
BMT Query on BMT	B [auth A]	L-PEPTIDE LINKING	C₁₀ H₁₉ N O₃		THR
MLE Query on MLE	B [auth A]	L-PEPTIDE LINKING	C₇ H₁₅ N O₂		LEU
MVA Query on MVA	B [auth A]	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		VAL
SAR Query on 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
R-Value Work: 0.184
R-Value Observed: 0.186
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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-11-21

Deposition Author(s):

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 (Full details and data files)

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