8V2Y

Room temperature X-ray Crystal Structure of FMN-bound long-chain flavodoxin from Rhodopseudomonas palustris

Summary for 8V2Y

• Entry DOI: 10.2210/pdb8v2y/pdb
• Descriptor: Flavodoxin, FLAVIN MONONUCLEOTIDE (3 entities in total)
• Functional Keywords: fmn-bound long chain flavodoxin, flavoprotein
• Biological source: Rhodopseudomonas palustris
• Total number of polymer chains: 2
• Total formula weight: 36682.33

Authors

Ansari, A.,Khan, S.A.,Miller, A.F. (deposition date: 2023-11-24, release date: 2024-03-13, Last modification date: 2024-04-03)

Primary citation

Khan, S.,Ansari, A.,Brachi, M.,Das, D.,El Housseini, W.,Minteer, S.,Miller, A.F.
Structure, dynamics, and redox reactivity of an all-purpose flavodoxin.
J.Biol.Chem., 300:107122-107122, 2024

PubMed Abstract: The flavodoxin of Rhodopseudomonas palustris CGA009 (Rp9Fld) supplies highly reducing equivalents to crucial enzymes such as hydrogenase, especially when the organism is iron-restricted. By acquiring those electrons from photodriven electron flow via the bifurcating electron transfer flavoprotein, Rp9Fld provides solar power to vital metabolic processes. To understand Rp9Fld's ability to work with diverse partners, we solved its crystal structure. We observed the canonical flavodoxin (Fld) fold and features common to other long-chain Flds but not all the surface loops thought to recognize partner proteins. Moreover, some of the loops display alternative structures and dynamics. To advance studies of protein-protein associations and conformational consequences, we assigned the F NMR signals of all five tyrosines (Tyrs). Our electrochemical measurements show that incorporation of 3-F-Tyr in place of Tyr has only a modest effect on Rp9Fld's redox properties even though Tyrs flank the flavin on both sides. Meanwhile, the F probes demonstrate the expected paramagnetic effect, with signals from nearby Tyrs becoming broadened beyond detection when the flavin semiquinone is formed. However, the temperature dependencies of chemical shifts and linewidths reveal dynamics affecting loops close to the flavin and regions that bind to partners in a variety of systems. These coincide with patterns of amino acid type conservation but not retention of specific residues, arguing against detailed specificity with respect to partners. We propose that the loops surrounding the flavin adopt altered conformations upon binding to partners and may even participate actively in electron transfer.

PubMed: 38417793
DOI: 10.1016/j.jbc.2024.107122

Experimental method

X-RAY DIFFRACTION (2.86 Å)