3AEQ

Structure of the light-independent protochlorophyllide reductase catalyzing a key reduction for greening in the dark

Summary for 3AEQ

• Entry DOI: 10.2210/pdb3aeq/pdb
• Related: 3AEK 3AER 3AES 3AET 3AEU
• Descriptor: Light-independent protochlorophyllide reductase subunit N, Light-independent protochlorophyllide reductase subunit B, IRON/SULFUR CLUSTER, ... (5 entities in total)
• Functional Keywords: iron/sulfur cluster, oxidoreductase, bacteriochlorophyll biosynthesis, chlorophyll biosynthesis, photosynthesis
• Biological source: Rhodobacter capsulatus; More
• Total number of polymer chains: 4
• Total formula weight: 211020.68

Authors

Muraki, N.,Nomata, J.,Shiba, T.,Fujita, Y.,Kurisu, G. (deposition date: 2010-02-10, release date: 2010-04-21, Last modification date: 2023-11-01)

Primary citation

Muraki, N.,Nomata, J.,Ebata, K.,Mizoguchi, T.,Shiba, T.,Tamiaki, H.,Kurisu, G.,Fujita, Y.
X-ray crystal structure of the light-independent protochlorophyllide reductase
Nature, 465:110-114, 2010

PubMed Abstract: Photosynthetic organisms adopt two different strategies for the reduction of the C17 = C18 double bond of protochlorophyllide (Pchlide) to form chlorophyllide a, the direct precursor of chlorophyll a (refs 1-4). The first involves the activity of the light-dependent Pchlide oxidoreductase, and the second involves the light-independent (dark-operative) Pchlide oxidoreductase (DPOR). DPOR is a nitrogenase-like enzyme consisting of two components, L-protein (a BchL dimer) and NB-protein (a BchN-BchB heterotetramer), which are structurally related to nitrogenase Fe protein and MoFe protein, respectively. Here we report the crystal structure of the NB-protein of DPOR from Rhodobacter capsulatus at a resolution of 2.3A. As expected, the overall structure is similar to that of nitrogenase MoFe protein: each catalytic BchN-BchB unit contains one Pchlide and one iron-sulphur cluster (NB-cluster) coordinated uniquely by one aspartate and three cysteines. Unique aspartate ligation is not necessarily needed for the cluster assembly but is essential for the catalytic activity. Specific Pchlide-binding accompanies the partial unwinding of an alpha-helix that belongs to the next catalytic BchN-BchB unit. We propose a unique trans-specific reduction mechanism in which the distorted C17-propionate of Pchlide and an aspartate from BchB serve as proton donors for C18 and C17 of Pchlide, respectively. Intriguingly, the spatial arrangement of the NB-cluster and Pchlide is almost identical to that of the P-cluster and FeMo-cofactor in nitrogenase MoFe-protein, illustrating that a common architecture exists to reduce chemically stable multibonds of porphyrin and dinitrogen.

PubMed: 20400946
DOI: 10.1038/nature08950

Experimental method

X-RAY DIFFRACTION (2.9 Å)