8FJD

Structure of chlorophyllase from Triticum aestivum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.46 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.266 

Starting Model: in silico
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A structure-function analysis of chlorophyllase reveals a mechanism for activity regulation dependent on disulfide bonds.

Jo, M.Knapp, M.Boggs, D.G.Brimberry, M.Donnan, P.H.Bridwell-Rabb, J.

(2023) J Biol Chem 299: 102958-102958

  • DOI: https://doi.org/10.1016/j.jbc.2023.102958
  • Primary Citation of Related Structures:  
    8FJD

  • PubMed Abstract: 

    Chlorophyll pigments are used by photosynthetic organisms to facilitate light capture and mediate the conversion of sunlight into chemical energy. Due to the indispensable nature of this pigment and its propensity to form reactive oxygen species, organisms heavily invest in its biosynthesis, recycling, and degradation. One key enzyme implicated in these processes is chlorophyllase, an α/β hydrolase that hydrolyzes the phytol tail of chlorophyll pigments to produce chlorophyllide molecules. This enzyme was discovered a century ago, but despite its importance to diverse photosynthetic organisms, there are still many missing biochemical details regarding how chlorophyllase functions. Here, we present the 4.46-Å resolution crystal structure of chlorophyllase from Triticum aestivum. This structure reveals the dimeric architecture of chlorophyllase, the arrangement of catalytic residues, an unexpected divalent metal ion-binding site, and a substrate-binding site that can accommodate a diverse range of pigments. Further, this structure exhibits the existence of both intermolecular and intramolecular disulfide bonds. We investigated the importance of these architectural features using enzyme kinetics, mass spectrometry, and thermal shift assays. Through this work, we demonstrated that the oxidation state of the Cys residues is imperative to the activity and stability of chlorophyllase, illuminating a biochemical trigger for responding to environmental stress. Additional bioinformatics analysis of the chlorophyllase enzyme family reveals widespread conservation of key catalytic residues and the identified "redox switch" among other plant chlorophyllase homologs, thus revealing key details regarding the structure-function relationships in chlorophyllase.


  • Organizational Affiliation

    Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyllase
A, B
325Triticum aestivumMutation(s): 0 
UniProt
Find proteins for A0A3B6QC98 (Triticum aestivum)
Explore A0A3B6QC98 
Go to UniProtKB:  A0A3B6QC98
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3B6QC98
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.46 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.266 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 197.52α = 90
b = 197.52β = 90
c = 96.83γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-SC0021240

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-08
    Type: Initial release
  • Version 1.1: 2023-02-15
    Changes: Database references
  • Version 1.2: 2023-03-15
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Refinement description