Does the crystal structure of vanadium nitrogenase contain a reaction intermediate? Evidence from quantum refinement
Cao, Lili LU ; Caldararu, Octav LU and Ryde, Ulf LU
(2020)
In Journal of Biological Inorganic Chemistry
25(6).
p.847-861
- Abstract
Abstract: Recently, a crystal structure of V-nitrogenase was presented, showing that one of the µ2 sulphide ions in the active site (S2B) is replaced by a lighter atom, suggested to be NH or NH2, i.e. representing a reaction intermediate. Moreover, a sulphur atom is found 7 Å from the S2B site, suggested to represent a storage site for this ion when it is displaced. We have re-evaluated this structure with quantum refinement, i.e. standard crystallographic refinement in which the empirical restraints (employed to ensure that the final structure makes chemical sense) are replaced by more accurate quantum–mechanical calculations. This allows us to test various interpretations of the structure, employing... (More)
Abstract: Recently, a crystal structure of V-nitrogenase was presented, showing that one of the µ2 sulphide ions in the active site (S2B) is replaced by a lighter atom, suggested to be NH or NH2, i.e. representing a reaction intermediate. Moreover, a sulphur atom is found 7 Å from the S2B site, suggested to represent a storage site for this ion when it is displaced. We have re-evaluated this structure with quantum refinement, i.e. standard crystallographic refinement in which the empirical restraints (employed to ensure that the final structure makes chemical sense) are replaced by more accurate quantum–mechanical calculations. This allows us to test various interpretations of the structure, employing quantum–mechanical calculations to predict the ideal structure and to use crystallographic measures like the real-space Z-score and electron-density difference maps to decide which structure fits the crystallographic raw data best. We show that the structure contains an OH−-bound state, rather than an N2-derived reaction intermediate. Moreover, the structure shows dual conformations in the active site with ~ 14% undissociated S2B ligand, but the storage site seems to be fully occupied, weakening the suggestion that it represents a storage site for the dissociated ligand. Graphic abstract: [Figure not available: see fulltext.]
(Less)
- author
- Cao, Lili
LU
; Caldararu, Octav
LU
and Ryde, Ulf
LU
- organization
- publishing date
- 2020-09
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- Nitrogen fixation, Nitrogenase, QM/MM, Quantum refinement, S2B dissociation
- in
- Journal of Biological Inorganic Chemistry
- volume
- 25
- issue
- 6
- pages
- 15 pages
- publisher
- Springer
- external identifiers
-
- scopus:85089920249
- pmid:32856107
- ISSN
- 0949-8257
- DOI
- 10.1007/s00775-020-01813-z
- language
- English
- LU publication?
- yes
- id
- dfc1c656-b807-4ce9-a5af-db60a9af443f
- date added to LUP
- 2020-09-07 13:11:28
- date last changed
- 2024-05-15 17:21:57
@article{dfc1c656-b807-4ce9-a5af-db60a9af443f,
abstract = {{<p>Abstract: Recently, a crystal structure of V-nitrogenase was presented, showing that one of the µ<sub>2</sub> sulphide ions in the active site (S2B) is replaced by a lighter atom, suggested to be NH or NH<sub>2</sub>, i.e. representing a reaction intermediate. Moreover, a sulphur atom is found 7 Å from the S2B site, suggested to represent a storage site for this ion when it is displaced. We have re-evaluated this structure with quantum refinement, i.e. standard crystallographic refinement in which the empirical restraints (employed to ensure that the final structure makes chemical sense) are replaced by more accurate quantum–mechanical calculations. This allows us to test various interpretations of the structure, employing quantum–mechanical calculations to predict the ideal structure and to use crystallographic measures like the real-space Z-score and electron-density difference maps to decide which structure fits the crystallographic raw data best. We show that the structure contains an OH<sup>−</sup>-bound state, rather than an N<sub>2</sub>-derived reaction intermediate. Moreover, the structure shows dual conformations in the active site with ~ 14% undissociated S2B ligand, but the storage site seems to be fully occupied, weakening the suggestion that it represents a storage site for the dissociated ligand. Graphic abstract: [Figure not available: see fulltext.]</p>}},
author = {{Cao, Lili and Caldararu, Octav and Ryde, Ulf}},
issn = {{0949-8257}},
keywords = {{Nitrogen fixation; Nitrogenase; QM/MM; Quantum refinement; S2B dissociation}},
language = {{eng}},
number = {{6}},
pages = {{847--861}},
publisher = {{Springer}},
series = {{Journal of Biological Inorganic Chemistry}},
title = {{Does the crystal structure of vanadium nitrogenase contain a reaction intermediate? Evidence from quantum refinement}},
url = {{https://lup.lub.lu.se/search/files/84187598/vcryst_269.pdf}},
doi = {{10.1007/s00775-020-01813-z}},
volume = {{25}},
year = {{2020}},
}