6TJR

Structure of HdrA-like subunit from Hyphomicrobium denitrificans

Summary for 6TJR

• Entry DOI: 10.2210/pdb6tjr/pdb
• Descriptor: Fumarate reductase/succinate dehydrogenase flavoprotein domain protein, IRON/SULFUR CLUSTER, FLAVIN-ADENINE DINUCLEOTIDE, ... (5 entities in total)
• Functional Keywords: heterodisulfide reductase, electron bifurcation, dissimilatory sulfur oxidation, fad, flavoprotein
• Biological source: Hyphomicrobium denitrificans
• Total number of polymer chains: 2
• Total formula weight: 78834.86

Authors

Kayastha, K.,Ermler, U.,Dahl, C. (deposition date: 2019-11-26, release date: 2020-08-19, Last modification date: 2024-05-15)

Primary citation

Ernst, C.,Kayastha, K.,Koch, T.,Venceslau, S.S.,Pereira, I.A.C.,Demmer, U.,Ermler, U.,Dahl, C.
Structural and spectroscopic characterization of a HdrA-like subunit from Hyphomicrobium denitrificans.
Febs J., 288:1664-1678, 2021

PubMed Abstract: Many bacteria and archaea employ a novel pathway of sulfur oxidation involving an enzyme complex that is related to the heterodisulfide reductase (Hdr or HdrABC) of methanogens. As a first step in the biochemical characterization of Hdr-like proteins from sulfur oxidizers (sHdr), we structurally analyzed the recombinant sHdrA protein from the Alphaproteobacterium Hyphomicrobium denitrificans at 1.4 Å resolution. The sHdrA core structure is similar to that of methanogenic HdrA (mHdrA) which binds the electron-bifurcating flavin adenine dinucleotide (FAD), the heart of the HdrABC-[NiFe]-hydrogenase catalyzed reaction. Each sHdrA homodimer carries two FADs and two [4Fe-4S] clusters being linked by electron conductivity. Redox titrations monitored by electron paramagnetic resonance and visible spectroscopy revealed a redox potential between -203 and -188 mV for the [4Fe-4S] center. The potentials for the FADH•/FADH and FAD/FADH• pairs reside between -174 and -156 mV and between -81 and -19 mV, respectively. The resulting stable semiquinone FADH• species already detectable in the visible and electron paramagnetic resonance spectra of the as-isolated state of sHdrA is incompatible with basic principles of flavin-based electron bifurcation such that the sHdr complex does not apply this new mode of energy coupling. The inverted one-electron FAD redox potentials of sHdr and mHdr are clearly reflected in the different FAD-polypeptide interactions. According to this finding and the assumption that the sHdr complex forms an asymmetric HdrAA'B1C1B2C2 hexamer, we tentatively propose a mechanism that links protein-bound sulfane oxidation to sulfite on HdrB1 with NAD reduction via lipoamide disulfide reduction on HdrB2. The FAD of HdrA thereby serves as an electron storage unit. DATABASE: Structural data are available in PDB database under the accession number 6TJR.

PubMed: 32750208
DOI: 10.1111/febs.15505

Experimental method

X-RAY DIFFRACTION (1.43 Å)