6TPO

Conformation of cd1 nitrite reductase NirS without bound heme d1

Summary for 6TPO

• Entry DOI: 10.2210/pdb6tpo/pdb
• Descriptor: Nitrite reductase, PENTAETHYLENE GLYCOL, (R,R)-2,3-BUTANEDIOL, ... (5 entities in total)
• Functional Keywords: cd1 nitrite reductase, nirs, oxidoreductase
• Biological source: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
• Total number of polymer chains: 1
• Total formula weight: 61205.95

Authors

Kluenemann, T.,Blankenfeldt, W. (deposition date: 2019-12-13, release date: 2020-11-18, Last modification date: 2024-11-06)

Primary citation

Klunemann, T.,Blankenfeldt, W.
Structure of heme d 1 -free cd 1 nitrite reductase NirS.
Acta Crystallogr.,Sect.F, 76:250-256, 2020

PubMed Abstract: A key step in anaerobic nitrate respiration is the reduction of nitrite to nitric oxide, which is catalysed by the cd nitrite reductase NirS in, for example, the Gram-negative opportunistic pathogen Pseudomonas aeruginosa. Each subunit of this homodimeric enzyme consists of a cytochrome c domain and an eight-bladed β-propeller that binds the uncommon isobacteriochlorin heme d as an essential part of its active site. Although NirS has been well studied mechanistically and structurally, the focus of previous studies has been on the active heme d-bound form. The heme d-free form of NirS reported here, which represents a premature state of the reductase, adopts an open conformation with the cytochrome c domains moved away from each other with respect to the active enzyme. Further, the movement of a loop around Trp498 seems to be related to a widening of the propeller, allowing easier access to the heme d-binding side. Finally, a possible link between the open conformation of NirS and flagella formation in P. aeruginosa is discussed.

PubMed: 32510465
DOI: 10.1107/S2053230X20006676

Experimental method

X-RAY DIFFRACTION (1.861 Å)