Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural basis of menaquinone reduction by succinate dehydrogenase from Chloroflexus aurantiacus.
Journal, issue, pages	Nat Commun, Vol. 16, Issue 1, Page 10782, Year 2025
Publish date	Nov 28, 2025
Authors	Xin Zhang / Jingyi Wu / Jiamao Wang / Huimin He / Aokun Liu / Xin Hong / Yuanyi Yu / Xinkai Pei / Xianjie Fang / Yueyong Xin / Lu Yu / Changlin Tian / Xiaoling Xu /
PubMed Abstract	Succinate: menaquinone oxidoreductase (SQR) couples the oxidation of succinate with the reduction of menaquinone (MK) as part of the TCA cycle and the aerobic respiratory chain in MK-containing ...Succinate: menaquinone oxidoreductase (SQR) couples the oxidation of succinate with the reduction of menaquinone (MK) as part of the TCA cycle and the aerobic respiratory chain in MK-containing bacteria and archaea. Despite its significance, questions persist regarding the electron and proton transfer mechanisms that drive the endergonic MK reduction by succinate. In this study, we determine cryo-EM structures of succinate dehydrogenase (SDH) from Chloroflexus aurantiacus (CaSDH), a facultative filamentous anoxygenic phototroph (FAP) that forms one of the earliest branches of photosynthetic bacteria. The structures of trimeric CaSDH, resolved in both apo- and MK-bound forms, reveal a single membrane-anchoring subunit containing two b-type hemes, a canonical Q site, and a Q site with atypical location, configuration and specificity, each bound to MK molecules. Using structural analysis, EPR, and enzymatic assays, we uncover electron transfer pathways connecting succinate oxidation to MK reduction at the Q and Q sites. These findings provide structural insights into the electron and proton transfer mechanisms of MK-dependent diheme SQRs and establish a foundation for structure-based inhibitor design and antibacterial drug development targeting these enzymes.
External links	Nat Commun / PubMed:41315263 / PubMed Central
Methods	EM (single particle)
Resolution	2.62 - 2.9 Å
Structure data	62932 9lay EMDB-62932, PDB-9lay: Cryo-EM structure of the apo-form succinate dehydrogenase from Chloroflexus aurantiacus Method: EM (single particle) / Resolution: 2.62 Å 62933 9laz EMDB-62933, PDB-9laz: Cryo-EM structure of the lipid-bound succiante dehydrogenase from Chloroflexus aurantiacus Method: EM (single particle) / Resolution: 2.69 Å 62934 9lb0 EMDB-62934, PDB-9lb0: Cryo-EM structure of the MK7-bound succinate dehydrogenase from Chloroflexus aurantiacus Method: EM (single particle) / Resolution: 2.74 Å 62935 9lb1 EMDB-62935, PDB-9lb1: Cryo-EM structure of the MK4-bound succinate dehydrogenase from Chloroflexus aurantiacus Method: EM (single particle) / Resolution: 2.9 Å
Chemicals	ChemComp-FAD: FLAVIN-ADENINE DINUCLEOTIDE / FADYM ChemComp-SIN: SUCCINIC ACID ChemComp-SF4: IRON/SULFUR CLUSTER ChemComp-FES: FE2/S2 (INORGANIC) CLUSTER ChemComp-F3S: FE3-S4 CLUSTER ChemComp-HEM: PROTOPORPHYRIN IX CONTAINING FE ChemComp-LMT: DODECYL-BETA-D-MALTOSIDE / detergentYM ChemComp-PGV: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / phospholipidYM ChemComp-PEV: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / POPE, phospholipidYM ChemComp-MQ7: MENAQUINONE-7 ChemComp-1L3: Menaquinone-4
Source	chloroflexus aurantiacus j-10-fl (bacteria)
Keywords	MEMBRANE PROTEIN / Succinate: menaquinone oxidoreductase; membrane protein; complex II; electron transfer; MEMBRANE PROTEIN / succinate: menaquinone oxidoreductase; succinate dehydrogenase; electron transfer; MEMBRANE PROTEIN / Succinate: menaquinone oxidoreductase; 3-hydroxypropionate cycle; succinate dehydrogenase;electron transfer