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5gv8

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Structure of NADH-cytochrome b5 reductase refined with the multipolar atomic model at 0.78A

Structural highlights

5gv8 is a 1 chain structure with sequence from Sus scrofa. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 0.78Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NB5R3_PIG Desaturation and elongation of fatty acids, cholesterol biosynthesis, drug metabolism, and, in erythrocyte, methemoglobin reduction.[:]

Publication Abstract from PubMed

Flavin compounds such as flavin adenine dinucleotide (FAD), flavin mononucleotide and riboflavin make up the active centers in flavoproteins that facilitate various oxidoreductive processes. The fine structural features of the hydrogens and valence electrons of the flavin molecules in the protein environment are critical to the functions of the flavoproteins. However, information on these features cannot be obtained from conventional protein X-ray analyses at ordinary resolution. Here we report the charge density analysis of a flavoenzyme, NADH-cytochrome b5 reductase (b5R), at an ultra-high resolution of 0.78 A. Valence electrons on the FAD cofactor as well as the peptide portion, which are clearly visualized even after the conventional refinement, are analyzed by the multipolar atomic model refinement. The topological analysis for the determined electron density reveals the valence electronic structure of the isoalloxazine ring of FAD and hydrogen-bonding interactions with the protein environment. The tetrahedral electronic distribution around the N5 atom of FAD in b5R is stabilized by hydrogen bonding with CalphaH of Tyr65 and amide-H of Thr66. The hydrogen bonding network leads to His49 composing the cytochrome b5-binding site via non-classical hydrogen bonds between N5 of FAD and CalphaH of Tyr65 and O of Tyr65 and CbetaH of His49.

Distribution of valence electrons of the flavin cofactor in NADH-cytochrome b5 reductase.,Takaba K, Takeda K, Kosugi M, Tamada T, Miki K Sci Rep. 2017 Feb 22;7:43162. doi: 10.1038/srep43162. PMID:28225078^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Takaba K, Takeda K, Kosugi M, Tamada T, Miki K. Distribution of valence electrons of the flavin cofactor in NADH-cytochrome b5 reductase. Sci Rep. 2017 Feb 22;7:43162. doi: 10.1038/srep43162. PMID:28225078 doi:http://dx.doi.org/10.1038/srep43162