Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 59.36 kDa 
• Atom Count: 4066 
• Modelled Residue Count: 445 
• Deposited Residue Count: 519 
• Unique protein chains: 1

6J95

Crystal structure of CYP97A3 in complex with retinal

• PDB DOI: 10.2210/pdb6J95/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2019-01-22 Released: 2020-01-22 
• Deposition Author(s): Niu, G., Guo, Q., Wang, J., Zhao, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.197 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 

Literature

Structural basis for plant lutein biosynthesis from alpha-carotene.

Niu, G., Guo, Q., Wang, J., Zhao, S., He, Y., Liu, L.

(2020) Proc Natl Acad Sci U S A 117: 14150-14157

• PubMed: 32513704 
• DOI: 10.1073/pnas.2001806117
• Primary Citation of Related Structures:  
  6J94, 6J95, 6L8H, 6L8I, 6L8J


• PubMed Abstract: 
  

Two cytochrome P450 enzymes, CYP97A3 and CYP97C1, catalyze hydroxylations of the β- and ε-rings of α-carotene to produce lutein. Chirality is introduced at the C-3 atom of both rings, and the reactions are both pro-3 R -stereospecific. We determined the crystal structures of CYP97A3 in substrate-free and complex forms with a nonnatural substrate and the structure of CYP97C1 in a detergent-bound form. The structures of CYP97A3 in different states show the substrate channel and the structure of CYP97C1 bound with octylthioglucoside confirms the binding site for the carotenoid substrate. Biochemical assays confirm that the ferredoxin-NADP ⁺ reductase (FNR)-ferredoxin pair is used as the redox partner. Details of the pro-3 R stereospecificity are revealed in the retinal-bound CYP97A3 structure. Further analysis indicates that the CYP97B clan bears similarity to the β-ring-specific CYP97A clan. Overall, our research describes the molecular basis for the last steps of lutein biosynthesis.

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Organizational Affiliation: 

School of Life Sciences, Anhui University, Hefei, Anhui 230601, China [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein LUTEIN DEFICIENT 5, chloroplastic	A	519	Arabidopsis thaliana	Mutation(s): 0  Gene Names: CYP97A3, LUT5, At1g31800, F5M6.19 EC: 1.14 Membrane Entity: Yes
UniProt
Find proteins for Q93VK5 (Arabidopsis thaliana) Explore Q93VK5  Go to UniProtKB:  Q93VK5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
RET	C [auth A]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
RET	Binding MOAD:  6J95	Kd: 230 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.197 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.481	α = 90
b = 82.097	β = 90
c = 110.339	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2019-01-22 
• Released Date: 2020-01-22 
Deposition Author(s): Niu, G., Guo, Q., Wang, J., Zhao, S.

Revision History  

• Version 1.0: 2020-01-22
  Type: Initial release
  
• Version 1.1: 2020-06-10
  Changes: Database references
• Version 1.2: 2020-06-24
  Changes: Database references
• Version 1.3: 2020-07-08
  Changes: Database references