PDBsum entry 5ofc

Oxidoreductase

PDB id: 5ofc

Contents

Protein chain

334 a.a.

Ligands

NO2

ACT

Metals

_CU ×2

Waters ×130

PDB id:

5ofc

Name:

Oxidoreductase

Title:

Cu nitrite reductase serial data at varying temperatures 190k 21.65mgy

Structure:

Copper-containing nitrite reductase. Chain: a. Synonym: cu-nir. Engineered: yes

Source:

Achromobacter cycloclastes. Organism_taxid: 223. Gene: nirk. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.68Å R-factor: 0.199 R-free: 0.228

Authors:

S.Horrell,D.Kekilli,R.W.Strange,M.A.Hough

Key ref:

S.Horrell et al. (2018). Enzyme catalysis captured using multiple structures from one crystal at varying temperatures. IUCrJ, 5, 283-292. PubMed id: 29755744

Date:

10-Jul-17 Release date: 23-May-18

Protein chain

P25006  (NIR_ACHCY) -  Copper-containing nitrite reductase from Achromobacter cycloclastes

Seq: 378 a.a.

Struc: 334 a.a.

Enzyme reactions

• Enzyme class: E.C.1.7.2.1 - nitrite reductase (NO-forming).
• Reaction: nitric oxide + Fe(III)-[cytochrome c] + H2O = Fe(II)-[cytochrome c] + nitrite + 2 H⁺

nitric oxide + Fe(III)-[cytochrome c] + H2O = Fe(II)-[cytochrome c] + nitrite + 2 × H(+) (Bound ligand (Het Group name = NO2) corresponds exactly)

• Cofactor: Cu cation or Fe cation; FAD

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

IUCrJ 5:283-292 (2018)

PubMed id: 29755744

Enzyme catalysis captured using multiple structures from one crystal at varying temperatures.

S.Horrell, D.Kekilli, K.Sen, R.L.Owen, F.S.N.Dworkowski, S.V.Antonyuk, T.W.Keal, C.W.Yong, R.R.Eady, S.S.Hasnain, R.W.Strange, M.A.Hough.

ABSTRACT

High-resolution crystal structures of enzymes in relevant redox states have transformed our understanding of enzyme catalysis. Recent developments have demonstrated that X-rays can be used, via the generation of solvated electrons, to drive reactions in crystals at cryogenic temperatures (100 K) to generate 'structural movies' of enzyme reactions. However, a serious limitation at these temperatures is that protein conformational motion can be significantly supressed. Here, the recently developed MSOX (multiple serial structures from one crystal) approach has been applied to nitrite-bound copper nitrite reductase at room temperature and at 190 K, close to the glass transition. During both series of multiple structures, nitrite was initially observed in a 'top-hat' geometry, which was rapidly transformed to a 'side-on' configuration before conversion to side-on NO, followed by dissociation of NO and substitution by water to reform the resting state. Density functional theory calculations indicate that the top-hat orientation corresponds to the oxidized type 2 copper site, while the side-on orientation is consistent with the reduced state. It is demonstrated that substrate-to-product conversion within the crystal occurs at a lower radiation dose at 190 K, allowing more of the enzyme catalytic cycle to be captured at high resolution than in the previous 100 K experiment. At room temperature the reaction was very rapid, but it remained possible to generate and characterize several structural states. These experiments open up the possibility of obtaining MSOX structural movies at multiple temperatures (MSOX-VT), providing an unparallelled level of structural information during catalysis for redox enzymes.