8P8G

Nitrogenase MoFe protein from A. vinelandii beta double mutant D353G/D357G

PDB DOI: https://doi.org/10.2210/pdb8P8G/pdb

Classification: OXIDOREDUCTASE
Organism(s): Azotobacter vinelandii DJ
Expression System: Azotobacter vinelandii DJ
Mutation(s): Yes

Deposited: 2023-06-01 Released: 2023-12-13
Deposition Author(s): Maslac, N., Wagner, T.
Funding Organization(s): Max Planck Society, German Research Foundation (DFG), Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.187
R-Value Work: 0.155
R-Value Observed: 0.157

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

The Mononuclear Metal-Binding Site of Mo-Nitrogenase Is Not Required for Activity.

Cadoux, C., Maslac, N., Di Luzio, L., Ratcliff, D., Gu, W., Wagner, T., Milton, R.D.

(2023) JACS Au 3: 2993-2999

PubMed: 38034976 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/jacsau.3c00567
Primary Citation of Related Structures:
8P8G

PubMed Abstract:
The biological N ₂-fixation process is catalyzed exclusively by metallocofactor-containing nitrogenases. Structural and spectroscopic studies highlighted the presence of an additional mononuclear metal-binding (MMB) site, which can coordinate Fe in addition to the two metallocofactors required for the reaction. This MMB site is located 15-Å from the active site, at the interface of two NifK subunits. The enigmatic function of the MMB site and its implications for metallocofactor installation, catalysis, electron transfer, or structural stability are investigated in this work. The axial ligands coordinating the additional Fe are almost universally conserved in Mo-nitrogenases, but a detailed observation of the available structures indicates a variation in occupancy or a metal substitution. A nitrogenase variant in which the MMB is disrupted was generated and characterized by X-ray crystallography, biochemistry, and enzymology. The crystal structure refined to 1.55-Å revealed an unambiguous loss of the metal site, also confirmed by an absence of anomalous signal for Fe. The position of the surrounding side chains and the overall architecture are superposable with the wild-type structure. Accordingly, the biochemical and enzymatic properties of the variant are similar to those of the wild-type nitrogenase, indicating that the MMB does not impact nitrogenase's activity and stability in vitro .

Organizational Affiliation

Department of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland.

Macromolecule Content

Total Structure Weight: 238.98 kDa
Atom Count: 18,458
Modelled Residue Count: 1,998
Deposited Residue Count: 2,046
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase protein alpha chain	A, C	500	Azotobacter vinelandii DJ	Mutation(s): 0 Gene Names: nifD EC: 1.18.6.1
UniProt
Find proteins for P07328 (Azotobacter vinelandii) Explore P07328 Go to UniProtKB: P07328
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07328
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase molybdenum-iron protein beta chain	B, D	523	Azotobacter vinelandii DJ	Mutation(s): 2 Gene Names: nifK, Avin_01400 EC: 1.18.6.1
UniProt
Find proteins for P07329 (Azotobacter vinelandii) Explore P07329 Go to UniProtKB: P07329
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07329
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ICS (Subject of Investigation/LOI) Query on ICS Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain H [auth A] MOL2 format, chain BA [auth C] MOL2 format, chain H [auth A] mmCIF format, chain BA [auth C] mmCIF format, chain H [auth A]	BA [auth C], H [auth A]	iron-sulfur-molybdenum cluster with interstitial carbon C Fe₇ Mo S₉ DDQFAOMIVKLFON-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain H [auth A] Interactions & Density Focus chain BA [auth C] Focus chain H [auth A]
CLF (Subject of Investigation/LOI) Query on CLF Download Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain X [auth B] MOL2 format, chain AB [auth D] MOL2 format, chain X [auth B] mmCIF format, chain AB [auth D] mmCIF format, chain X [auth B]	AB [auth D], X [auth B]	FE(8)-S(7) CLUSTER Fe₈ S₇ JKVMXLBGZBULKV-UHFFFAOYSA-N		Interactions Focus chain AB [auth D] Focus chain X [auth B] Interactions & Density Focus chain AB [auth D] Focus chain X [auth B]
1CL (Subject of Investigation/LOI) Query on 1CL Download Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain ZA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain ZA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain ZA [auth D]	W [auth B], ZA [auth D]	FE(8)-S(7) CLUSTER, OXIDIZED Fe₈ S₇ JKVMXLBGZBULKV-UHFFFAOYSA-N		Interactions Focus chain W [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain W [auth B] Focus chain ZA [auth D]
HCA (Subject of Investigation/LOI) Query on HCA Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain G [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain G [auth A] mmCIF format, chain AA [auth C] mmCIF format, chain G [auth A]	AA [auth C], G [auth A]	3-HYDROXY-3-CARBOXY-ADIPIC ACID C₇ H₁₀ O₇ XKJVEVRQMLKSMO-SSDOTTSWSA-N		Interactions Focus chain AA [auth C] Focus chain G [auth A] Interactions & Density Focus chain AA [auth C] Focus chain G [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain U [auth B] MOL2 format, chain U [auth B] mmCIF format, chain U [auth B]	U [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain U [auth B] Interactions & Density Focus chain U [auth B]
DIO Query on DIO Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain UA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain UA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain UA [auth D]	R [auth B], UA [auth D]	1,4-DIETHYLENE DIOXIDE C₄ H₈ O₂ RYHBNJHYFVUHQT-UHFFFAOYSA-N		Interactions Focus chain R [auth B] Focus chain UA [auth D] Interactions & Density Focus chain R [auth B] Focus chain UA [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain E [auth A] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain K [auth B] SDF format, chain KA [auth D] SDF format, chain L [auth B] SDF format, chain LA [auth D] SDF format, chain M [auth B] SDF format, chain MA [auth D] SDF format, chain N [auth B] SDF format, chain NA [auth D] SDF format, chain O [auth B] SDF format, chain OA [auth D] SDF format, chain P [auth B] SDF format, chain PA [auth D] SDF format, chain Q [auth B] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain S [auth B] SDF format, chain SA [auth D] SDF format, chain T [auth B] SDF format, chain TA [auth D] SDF format, chain V [auth B] SDF format, chain VA [auth D] SDF format, chain WA [auth D] SDF format, chain XA [auth D] SDF format, chain YA [auth D] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth B] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth B] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth B] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth B] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain XA [auth D] MOL2 format, chain YA [auth D] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth B] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth B] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth B] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth B] mmCIF format, chain NA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth D] mmCIF format, chain WA [auth D] mmCIF format, chain XA [auth D] mmCIF format, chain YA [auth D]	CA [auth C] DA [auth C] E [auth A] EA [auth C] FA [auth C] CA [auth C], DA [auth C], E [auth A], EA [auth C], FA [auth C], GA [auth C], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth D], K [auth B], KA [auth D], L [auth B], LA [auth D], M [auth B], MA [auth D], N [auth B], NA [auth D], O [auth B], OA [auth D], P [auth B], PA [auth D], Q [auth B], QA [auth D], RA [auth D], S [auth B], SA [auth D], T [auth B], TA [auth D], V [auth B], VA [auth D], WA [auth D], XA [auth D], YA [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth B] Focus chain KA [auth D] Focus chain L [auth B] Focus chain LA [auth D] Focus chain M [auth B] Focus chain MA [auth D] Focus chain N [auth B] Focus chain NA [auth D] Focus chain O [auth B] Focus chain OA [auth D] Focus chain P [auth B] Focus chain PA [auth D] Focus chain Q [auth B] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain YA [auth D] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth B] Focus chain KA [auth D] Focus chain L [auth B] Focus chain LA [auth D] Focus chain M [auth B] Focus chain MA [auth D] Focus chain N [auth B] Focus chain NA [auth D] Focus chain O [auth B] Focus chain OA [auth D] Focus chain P [auth B] Focus chain PA [auth D] Focus chain Q [auth B] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain YA [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain Y [auth C] MOL2 format, chain F [auth A] MOL2 format, chain Y [auth C] mmCIF format, chain F [auth A] mmCIF format, chain Y [auth C]	F [auth A], Y [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain Y [auth C] Interactions & Density Focus chain F [auth A] Focus chain Y [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain Z [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain Z [auth C]	Z [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain Z [auth C] Interactions & Density Focus chain Z [auth C]