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Title2.85 and 2.99 Å resolution structures of 110 kDa nitrite reductase determined by 200 kV cryogenic electron microscopy.
Journal, issue, pagesJ Struct Biol, Vol. 213, Issue 3, Page 107768, Year 2021
Publish dateJul 1, 2021
AuthorsNaruhiko Adachi / Takahide Yamaguchi / Toshio Moriya / Masato Kawasaki / Kotaro Koiwai / Akira Shinoda / Yusuke Yamada / Fumiaki Yumoto / Takamitsu Kohzuma / Toshiya Senda /
PubMed AbstractCu-containing nitrite reductases (NiRs) are 110 kDa enzymes that play central roles in denitrification. Although the NiRs have been well studied, with over 100 Protein Data Bank entries, such issues ...Cu-containing nitrite reductases (NiRs) are 110 kDa enzymes that play central roles in denitrification. Although the NiRs have been well studied, with over 100 Protein Data Bank entries, such issues as crystal packing, photoreduction, and lack of high pH cases have impeded structural analysis of their catalytic mechanisms. Here we show the cryogenic electron microscopy (cryo-EM) structures of Achromobacter cycloclastes NiR (AcNiR) at pH 6.2 and 8.1. The optimization of 3D-reconstruction parameters achieved 2.99 and 2.85 Å resolution. Comprehensive comparisons with cryo-EM and 56 AcNiR crystal structures suggested crystallographic artifacts in residues 185-215 and His255' due to packing and photoreduction, respectively. We used a newly developed map comparison method to detect structural change around the type 2 Cu site. While the theoretical estimation of coordinate errors of cryo-EM structures remains difficult, combined analysis using X-ray and cryo-EM structures will allow deeper insight into the local structural changes of proteins.
External linksJ Struct Biol / PubMed:34217801
MethodsEM (single particle)
Resolution2.85 - 2.99 Å
Structure data

0730

6knf

EMDB-0730, PDB-6knf:
CryoEM map and model of Nitrite Reductase at pH 6.2
Method: EM (single particle) / Resolution: 2.99 Å

0731

6kng

EMDB-0731, PDB-6kng:
CryoEM map and model of Nitrite Reductase at pH 8.1
Method: EM (single particle) / Resolution: 2.85 Å

Chemicals

ChemComp-CU:
COPPER (II) ION / Copper

Source
  • achromobacter cycloclastes (bacteria)
KeywordsOXIDOREDUCTASE / Cu containing nitrite reductase

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