2YNM image
Deposition Date 2012-10-16
Release Date 2013-01-30
Last Version Date 2023-12-20
Entry Detail
PDB ID:
2YNM
Keywords:
Title:
Structure of the ADPxAlF3-Stabilized Transition State of the Nitrogenase-like Dark-Operative Protochlorophyllide Oxidoreductase Complex from Prochlorococcus marinus with Its Substrate Protochlorophyllide a
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.10 Å
R-Value Free:
0.23
R-Value Work:
0.19
R-Value Observed:
0.20
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE IRON-SULFUR ATP-BINDING PROTEIN
Gene (Uniprot):chlL
Chain IDs:A, B
Chain Length:301
Number of Molecules:2
Biological Source:PROCHLOROCOCCUS MARINUS
Polymer Type:polypeptide(L)
Molecule:LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT N
Gene (Uniprot):chlN
Chain IDs:C
Chain Length:426
Number of Molecules:1
Biological Source:PROCHLOROCOCCUS MARINUS
Polymer Type:polypeptide(L)
Molecule:LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT B
Gene (Uniprot):chlB
Chain IDs:D
Chain Length:530
Number of Molecules:1
Biological Source:PROCHLOROCOCCUS MARINUS
Primary Citation
Structure of Adp-Aluminium Fluoride-Stabilized Protochlorophyllide Oxidoreductase Complex.
Proc.Natl.Acad.Sci.USA 110 2094 ? (2013)
PMID: 23341615 DOI: 10.1073/PNAS.1218303110

Abstact

Photosynthesis uses chlorophylls for the conversion of light into chemical energy, the driving force of life on Earth. During chlorophyll biosynthesis in photosynthetic bacteria, cyanobacteria, green algae and gymnosperms, dark-operative protochlorophyllide oxidoreductase (DPOR), a nitrogenase-like metalloenzyme, catalyzes the chemically challenging two-electron reduction of the fully conjugated ring system of protochlorophyllide a. The reduction of the C-17=C-18 double bond results in the characteristic ring architecture of all chlorophylls, thereby altering the absorption properties of the molecule and providing the basis for light-capturing and energy-transduction processes of photosynthesis. We report the X-ray crystallographic structure of the substrate-bound, ADP-aluminium fluoride-stabilized (ADP·AlF(3)-stabilized) transition state complex between the DPOR components L(2) and (NB)(2) from the marine cyanobacterium Prochlorococcus marinus. Our analysis permits a thorough investigation of the dynamic interplay between L(2) and (NB)(2). Upon complex formation, substantial ATP-dependent conformational rearrangements of L(2) trigger the protein-protein interactions with (NB)(2) as well as the electron transduction via redox-active [4Fe-4S] clusters. We also present the identification of artificial "small-molecule substrates" of DPOR in correlation with those of nitrogenase. The catalytic differences and similarities between DPOR and nitrogenase have broad implications for the energy transduction mechanism of related multiprotein complexes that are involved in the reduction of chemically stable double and/or triple bonds.

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