PDBsum entry 6tjr

Flavoprotein

PDB id: 6tjr

Contents

Protein chains

340 a.a.

Ligands

SF4 ×2

FAD ×2

MES ×5

Waters ×603

PDB id:

6tjr

Name:

Flavoprotein

Title:

Structure of hdra-like subunit from hyphomicrobium denitrificans

Structure:

Fumarate reductase/succinate dehydrogenase flavoprotein domain protein. Chain: a, b. Engineered: yes

Source:

Hyphomicrobium denitrificans. Organism_taxid: 53399. Gene: hden_0691. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: delta iscr

Resolution:

1.43Å R-factor: 0.164 R-free: 0.179

Authors:

K.Kayastha,U.Ermler,C.Dahl

Key ref:

C.Ernst et al. (2021). Structural and spectroscopic characterization of a HdrA-like subunit from Hyphomicrobium denitrificans. FEBS J, 288, 1664-1678. PubMed id: 32750208 DOI: 10.1111/febs.15505

Date:

26-Nov-19 Release date: 19-Aug-20

Protein chains

D8JT26  (D8JT26_HYPDA) -  Fumarate reductase/succinate dehydrogenase flavoprotein domain protein from Hyphomicrobium denitrificans (strain ATCC 51888 / DSM 1869 / NCIMB 11706 / TK 0415)

Seq: 349 a.a.

Struc: 340 a.a.

DOI no: 10.1111/febs.15505

FEBS J 288:1664-1678 (2021)

PubMed id: 32750208

Structural and spectroscopic characterization of a HdrA-like subunit from Hyphomicrobium denitrificans.

C.Ernst, K.Kayastha, T.Koch, S.S.Venceslau, I.A.C.Pereira, U.Demmer, U.Ermler, C.Dahl.

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.