6UYK

Dark-operative protochlorophyllide oxidoreductase in the nucleotide-free form.

Summary for 6UYK

• Entry DOI: 10.2210/pdb6uyk/pdb
• Descriptor: Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein, IRON/SULFUR CLUSTER, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: electron transfer, nitrogenase, dpor, photosynthesis, iron-sulfur cluster, oxidoreductase
• Biological source: Rhodobacter sphaeroides
• Total number of polymer chains: 4
• Total formula weight: 140175.55

Authors

Bacik, J.P.,Imran, S.M.S.,Watkins, M.B.,Corless, E.,Antony, E.,Ando, N. (deposition date: 2019-11-13, release date: 2020-12-02, Last modification date: 2023-10-11)

Primary citation

Corless, E.I.,Saad Imran, S.M.,Watkins, M.B.,Bacik, J.P.,Mattice, J.R.,Patterson, A.,Danyal, K.,Soffe, M.,Kitelinger, R.,Seefeldt, L.C.,Origanti, S.,Bennett, B.,Bothner, B.,Ando, N.,Antony, E.
The flexible N-terminus of BchL autoinhibits activity through interaction with its [4Fe-4S] cluster and released upon ATP binding.
J.Biol.Chem., 296:100107-100107, 2020

PubMed Abstract: A key step in bacteriochlorophyll biosynthesis is the reduction of protochlorophyllide to chlorophyllide, catalyzed by dark-operative protochlorophyllide oxidoreductase. Dark-operative protochlorophyllide oxidoreductase contains two [4Fe-4S]-containing component proteins (BchL and BchNB) that assemble upon ATP binding to BchL to coordinate electron transfer and protochlorophyllide reduction. But the precise nature of the ATP-induced conformational changes is poorly understood. We present a crystal structure of BchL in the nucleotide-free form where a conserved, flexible region in the N-terminus masks the [4Fe-4S] cluster at the docking interface between BchL and BchNB. Amino acid substitutions in this region produce a hyperactive enzyme complex, suggesting a role for the N-terminus in autoinhibition. Hydrogen-deuterium exchange mass spectrometry shows that ATP binding to BchL produces specific conformational changes leading to release of the flexible N-terminus from the docking interface. The release also promotes changes within the local environment surrounding the [4Fe-4S] cluster and promotes BchL-complex formation with BchNB. A key patch of amino acids, Asp-Phe-Asp (the 'DFD patch'), situated at the mouth of the BchL ATP-binding pocket promotes intersubunit cross stabilization of the two subunits. A linked BchL dimer with one defective ATP-binding site does not support protochlorophyllide reduction, illustrating nucleotide binding to both subunits as a prerequisite for the intersubunit cross stabilization. The masking of the [4Fe-4S] cluster by the flexible N-terminal region and the associated inhibition of the activity is a novel mechanism of regulation in metalloproteins. Such mechanisms are possibly an adaptation to the anaerobic nature of eubacterial cells with poor tolerance for oxygen.

PubMed: 33219127
DOI: 10.1074/jbc.RA120.016278

Experimental method

X-RAY DIFFRACTION (2.6 Å)