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	The active form of quinol-dependent nitric oxide reductase from is a dimer.
Journal, issue, pages	IUCrJ, Vol. 7, Issue Pt 3, Page 404-415, Year 2020
Publish date	May 1, 2020
Authors	M Arif M Jamali / Chai C Gopalasingam / Rachel M Johnson / Takehiko Tosha / Kazumasa Muramoto / Stephen P Muench / Svetlana V Antonyuk / Yoshitsugu Shiro / Samar S Hasnain /
PubMed Abstract	is carried by nearly a billion humans, causing developmental impairment and over 100 000 deaths a year. A quinol-dependent nitric oxide reductase (qNOR) plays a critical role in the survival of ... is carried by nearly a billion humans, causing developmental impairment and over 100 000 deaths a year. A quinol-dependent nitric oxide reductase (qNOR) plays a critical role in the survival of the bacterium in the human host. X-ray crystallographic analyses of qNOR, including that from (qNOR) reported here at 3.15 Å resolution, show monomeric assemblies, despite the more active dimeric sample being used for crystallization. Cryo-electron microscopic analysis of the same chromatographic fraction of qNOR, however, revealed a dimeric assembly at 3.06 Å resolution. It is shown that zinc (which is used in crystallization) binding near the dimer-stabilizing TMII region contributes to the disruption of the dimer. A similar destabilization is observed in the monomeric (∼85 kDa) cryo-EM structure of a mutant (Glu494Ala) qNOR from the opportunistic pathogen () , which primarily migrates as a monomer. The monomer-dimer transition of qNORs seen in the cryo-EM and crystallographic structures has wider implications for structural studies of multimeric membrane proteins. X-ray crystallographic and cryo-EM structural analyses have been performed on the same chromatographic fraction of qNOR to high resolution. This represents one of the first examples in which the two approaches have been used to reveal a monomeric assembly and a dimeric assembly in vitrified cryo-EM grids. A number of factors have been identified that may trigger the destabilization of helices that are necessary to preserve the integrity of the dimer. These include zinc binding near the entry of the putative proton-transfer channel and the preservation of the conformational integrity of the active site. The mutation near the active site results in disruption of the active site, causing an additional destabilization of helices (TMIX and TMX) that flank the proton-transfer channel helices, creating an inert monomeric enzyme.
External links	IUCrJ / PubMed:32431824 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	3.06 - 4.5 Å
Structure data	0822 6l3h EMDB-0822, PDB-6l3h: Cryo-EM structure of dimeric quinol dependent Nitric Oxide Reductase (qNOR) from the pathogen Neisseria meninigitidis Method: EM (single particle) / Resolution: 3.06 Å 10387 6t6v EMDB-10387, PDB-6t6v: Glu-494-Ala inactive monomer of a quinol dependent Nitric Oxide Reductase (qNOR) from Alcaligenes xylosoxidans Method: EM (single particle) / Resolution: 4.5 Å PDB-6l1x: Quinol-dependent nitric oxide reductase (qNOR) from Neisseria meningitidis in the monomeric oxidized state with zinc complex. Method: X-RAY DIFFRACTION / Resolution: 3.15 Å
Chemicals	ChemComp-HEM: PROTOPORPHYRIN IX CONTAINING FE / Heme B ChemComp-FE: Unknown entry / Iron ChemComp-CA: Unknown entry ChemComp-ZN: Unknown entry ChemComp-HOH: WATER / Water
Source	neisseria meningitidis alpha14 (bacteria) Achromobacter xylosoxidans (bacteria) alcaligenes xylosoxydans xylosoxydans (bacteria) neisseria meningitidis (strain alpha14) (bacteria)
Keywords	OXIDOREDUCTASE / reductase / membrane-bound / nitric oxide / Neisseria meningitidis / quinol-dependent electrogenic Nitric Oxide Reductase (qNOR) / Monomer / Proton Transfer