6R46 | pdb_00006r46

Crystal structure of LPOR (Thermosynechococcus elongatus) complexed with NADP+ at 2.5A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.249 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6R46

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structural basis for enzymatic photocatalysis in chlorophyll biosynthesis.

Zhang, S.Heyes, D.J.Feng, L.Sun, W.Johannissen, L.O.Liu, H.Levy, C.W.Li, X.Yang, J.Yu, X.Lin, M.Hardman, S.J.O.Hoeven, R.Sakuma, M.Hay, S.Leys, D.Rao, Z.Zhou, A.Cheng, Q.Scrutton, N.S.

(2019) Nature 574: 722-725

  • DOI: https://doi.org/10.1038/s41586-019-1685-2
  • Primary Citation Related Structures: 
    6R46, 6R48, 6RNV, 6RNW

  • PubMed Abstract: 

    The enzyme protochlorophyllide oxidoreductase (POR) catalyses a light-dependent step in chlorophyll biosynthesis that is essential to photosynthesis and, ultimately, all life on Earth 1-3 . POR, which is one of three known light-dependent enzymes 4,5 , catalyses reduction of the photosensitizer and substrate protochlorophyllide to form the pigment chlorophyllide. Despite its biological importance, the structural basis for POR photocatalysis has remained unknown. Here we report crystal structures of cyanobacterial PORs from Thermosynechococcus elongatus and Synechocystis sp. in their free forms, and in complex with the nicotinamide coenzyme. Our structural models and simulations of the ternary protochlorophyllide-NADPH-POR complex identify multiple interactions in the POR active site that are important for protochlorophyllide binding, photosensitization and photochemical conversion to chlorophyllide. We demonstrate the importance of active-site architecture and protochlorophyllide structure in driving POR photochemistry in experiments using POR variants and protochlorophyllide analogues. These studies reveal how the POR active site facilitates light-driven reduction of protochlorophyllide by localized hydride transfer from NADPH and long-range proton transfer along structurally defined proton-transfer pathways.


  • Organizational Affiliation
    • Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK.

Macromolecule Content 

  • Total Structure Weight: 37.02 kDa 
  • Atom Count: 2,217 
  • Modeled Residue Count: 275 
  • Deposited Residue Count: 322 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NADPH-protochlorophyllide oxidoreductase322Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: por
EC: 1.3.1.33
UniProt
Find proteins for Q8DLC1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DLC1 
Go to UniProtKB:  Q8DLC1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DLC1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP

Query on NAP



Download:Ideal Coordinates CCD File
B [auth A]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
J [auth A],
K [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.249 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.95α = 90
b = 134.95β = 90
c = 104.75γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-30
    Type: Initial release
  • Version 1.1: 2020-05-13
    Changes: Database references
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references, Derived calculations