7JK9

Helical filaments of plant light-dependent protochlorophyllide oxidoreductase (LPOR) bound to NADPH, Pchlide, and membrane

  • Classification: PHOTOSYNTHESIS
  • Organism(s): Arabidopsis thaliana
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2020-07-28 Released: 2021-03-17 
  • Deposition Author(s): Nguyen, H.C., Gabruk, M., Frost, A.
  • Funding Organization(s): Foundation for Polish Science, Ministry of Science and Higher Education (Poland), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Photocatalytic LPOR forms helical lattices that shape membranes for chlorophyll synthesis.

Nguyen, H.C.Melo, A.A.Kruk, J.Frost, A.Gabruk, M.

(2021) Nat Plants 7: 437-444

  • DOI: https://doi.org/10.1038/s41477-021-00885-2
  • Primary Citation of Related Structures:  
    7JK9

  • PubMed Abstract: 

    Chlorophyll biosynthesis, crucial to life on Earth, is tightly regulated because its precursors are phototoxic 1 . In flowering plants, the enzyme light-dependent protochlorophyllide oxidoreductase (LPOR) captures photons to catalyse the penultimate reaction: the reduction of a double bond within protochlorophyllide (Pchlide) to generate chlorophyllide (Chlide) 2,3 . In darkness, LPOR oligomerizes to facilitate photon energy transfer and catalysis 4,5 . However, the complete three-dimensional structure of LPOR, the higher-order architecture of LPOR oligomers and the implications of these self-assembled states for catalysis, including how LPOR positions Pchlide and the co-factor NADPH, remain unknown. Here, we report the atomic structure of LPOR assemblies by electron cryo-microscopy. LPOR polymerizes with its substrates into helical filaments around constricted lipid bilayer tubes. Portions of LPOR and Pchlide insert into the outer membrane leaflet, targeting the product, Chlide, to the membrane for the final reaction site of chlorophyll biosynthesis. In addition to its crucial photocatalytic role, we show that in darkness LPOR filaments directly shape membranes into high-curvature tubules with the spectral properties of the prolamellar body, whose light-triggered disassembly provides lipids for thylakoid assembly. Moreover, our structure of the catalytic site challenges previously proposed reaction mechanisms 6 . Together, our results reveal a new and unexpected synergy between photosynthetic membrane biogenesis and chlorophyll synthesis in plants, orchestrated by LPOR.


  • Organizational Affiliation

    Department of Biochemistry & Biophysics, Quantitative Biosciences Institute, University of California, San Francisco, CA, USA. nguyen.henry.c@gmail.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protochlorophyllide reductase B, chloroplastic401Arabidopsis thalianaMutation(s): 0 
Gene Names: PORBAt4g27440F27G19.40
EC: 1.3.1.33
UniProt
Find proteins for P21218 (Arabidopsis thaliana)
Explore P21218 
Go to UniProtKB:  P21218
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21218
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMG
Query on LMG

Download Ideal Coordinates CCD File 
AC [auth M]
AF [auth NA]
BD [auth W]
CB [auth E]
CE [auth FA]
AC [auth M],
AF [auth NA],
BD [auth W],
CB [auth E],
CE [auth FA],
DC [auth N],
DF [auth OA],
ED [auth X],
FB [auth F],
FE [auth GA],
GC [auth O],
HD [auth Y],
IB [auth G],
IE [auth HA],
JC [auth P],
KD [auth Z],
LB [auth H],
LE [auth IA],
MC [auth Q],
ND [auth AA],
OB [auth I],
OE [auth JA],
PC [auth R],
QA [auth A],
QD [auth BA],
RB [auth J],
RE [auth KA],
SC [auth S],
TA [auth B],
TD [auth CA],
UB [auth K],
UE [auth LA],
VC [auth T],
WA [auth C],
WD [auth DA],
XB [auth L],
XE [auth MA],
YC [auth V],
ZA [auth D],
ZD [auth EA]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
NDP
Query on NDP

Download Ideal Coordinates CCD File 
AB [auth E]
AE [auth FA]
BC [auth N]
BF [auth OA]
CD [auth X]
AB [auth E],
AE [auth FA],
BC [auth N],
BF [auth OA],
CD [auth X],
DB [auth F],
DE [auth GA],
EC [auth O],
FD [auth Y],
GB [auth G],
GE [auth HA],
HC [auth P],
ID [auth Z],
JB [auth H],
JE [auth IA],
KC [auth Q],
LD [auth AA],
MB [auth I],
ME [auth JA],
NC [auth R],
OA [auth A],
OD [auth BA],
PB [auth J],
PE [auth KA],
QC [auth S],
RA [auth B],
RD [auth CA],
SB [auth K],
SE [auth LA],
TC [auth T],
UA [auth C],
UD [auth DA],
VB [auth L],
VE [auth MA],
WC [auth V],
XA [auth D],
XD [auth EA],
YB [auth M],
YE [auth NA],
ZC [auth W]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
PMR (Subject of Investigation/LOI)
Query on PMR

Download Ideal Coordinates CCD File 
AD [auth W]
BB [auth E]
BE [auth FA]
CC [auth N]
CF [auth OA]
AD [auth W],
BB [auth E],
BE [auth FA],
CC [auth N],
CF [auth OA],
DD [auth X],
EB [auth F],
EE [auth GA],
FC [auth O],
GD [auth Y],
HB [auth G],
HE [auth HA],
IC [auth P],
JD [auth Z],
KB [auth H],
KE [auth IA],
LC [auth Q],
MD [auth AA],
NB [auth I],
NE [auth JA],
OC [auth R],
PA [auth A],
PD [auth BA],
QB [auth J],
QE [auth KA],
RC [auth S],
SA [auth B],
SD [auth CA],
TB [auth K],
TE [auth LA],
UC [auth T],
VA [auth C],
VD [auth DA],
WB [auth L],
WE [auth MA],
XC [auth V],
YA [auth D],
YD [auth EA],
ZB [auth M],
ZE [auth NA]
Protochlorophyllide
C35 H32 Mg N4 O5
ZHFORNQMLKGQNN-KKNVGXODSA-L
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Foundation for Polish SciencePoland024.2018
Ministry of Science and Higher Education (Poland)PolandPPN/BEK/2018/1/00105
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1DP2GM110772-01

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-17
    Type: Initial release
  • Version 1.1: 2021-10-06
    Changes: Database references