8BTS | pdb_00008bts

Nitrogenase MoFe protein from A. vinelandii alpha double mutant C45A/L158C

PDB DOI: https://doi.org/10.2210/pdb8BTS/pdb

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

Deposited: 2022-11-29 Released: 2023-06-07
Deposition Author(s): Wagner, T., Maslac, N.
Funding Organization(s): Swiss National Science Foundation, Max Planck Society, German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.03 Å
R-Value Free:
0.223 (Depositor), 0.221 (DCC)
R-Value Work:
0.204 (Depositor), 0.204 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Nitrogen Fixation and Hydrogen Evolution by Sterically Encumbered Mo-Nitrogenase.

Cadoux, C., Ratcliff, D., Maslac, N., Gu, W., Tsakoumagkos, I., Hoogendoorn, S., Wagner, T., Milton, R.D.

(2023) JACS Au 3: 1521-1533

PubMed: 37234119 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/jacsau.3c00165
Primary Citation Related Structures:
8BTS

PubMed Abstract:
The substrate-reducing proteins of all nitrogenases (MoFe, VFe, and FeFe) are organized as α ₂ß ₂(γ ₂) multimers with two functional halves. While their dimeric organization could afford improved structural stability of nitrogenases in vivo , previous research has proposed both negative and positive cooperativity contributions with respect to enzymatic activity. Here, a 1.4 kDa peptide was covalently introduced in the proximity of the P cluster, corresponding to the Fe protein docking position. The Strep-tag carried by the added peptide simultaneously sterically inhibits electron delivery to the MoFe protein and allows the isolation of partially inhibited MoFe proteins (where the half-inhibited MoFe protein was targeted). We confirm that the partially functional MoFe protein retains its ability to reduce N ₂ to NH ₃, with no significant difference in selectivity over obligatory/parasitic H ₂ formation. Our experiment concludes that wild-type nitrogenase exhibits negative cooperativity during the steady state regarding H ₂ and NH ₃ formation (under Ar or N ₂), with one-half of the MoFe protein inhibiting turnover in the second half. This emphasizes the presence and importance of long-range (>95 Å) protein-protein communication in biological N ₂ fixation in Azotobacter vinelandii .

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: 472.79 kDa
Atom Count: 32,158
Modeled Residue Count: 3,996
Deposited Residue Count: 4,092
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase protein alpha chain	A, C, E [auth H], G [auth J]	500	Azotobacter vinelandii DJ	Mutation(s): 2 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07328
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase molybdenum-iron protein beta chain	B, D, F [auth I], H [auth L]	523	Azotobacter vinelandii DJ	Mutation(s): 0 Gene Names: nifK EC: 1.18.6.1
UniProt
Find proteins for P07329 (Azotobacter vinelandii) Explore P07329 Go to UniProtKB: P07329
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07329
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 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 GA [auth H] SDF format, chain J [auth A] SDF format, chain MA [auth J] SDF format, chain X [auth C] MOL2 format, chain GA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain MA [auth J] MOL2 format, chain X [auth C] mmCIF format, chain GA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain MA [auth J] mmCIF format, chain X [auth C]	GA [auth H], J [auth A], MA [auth J], X [auth C]	iron-sulfur-molybdenum cluster with interstitial carbon C Fe₇ Mo S₉ DDQFAOMIVKLFON-UHFFFAOYSA-N		Interactions Focus chain GA [auth H] Focus chain J [auth A] Focus chain MA [auth J] Focus chain X [auth C] Interactions & Density Focus chain GA [auth H] Focus chain J [auth A] Focus chain MA [auth J] Focus chain X [auth C]
1CL (Subject of Investigation/LOI) Query on 1CL Download:Ideal Coordinates CCD File SDF format, chain PA [auth L] SDF format, chain N [auth B] SDF format, chain IA [auth I] SDF format, chain AA [auth D] MOL2 format, chain PA [auth L] MOL2 format, chain N [auth B] MOL2 format, chain IA [auth I] MOL2 format, chain AA [auth D] mmCIF format, chain PA [auth L] mmCIF format, chain N [auth B] mmCIF format, chain IA [auth I] mmCIF format, chain AA [auth D]	AA [auth D], IA [auth I], N [auth B], PA [auth L]	FE(8)-S(7) CLUSTER, OXIDIZED Fe₈ S₇ JKVMXLBGZBULKV-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain IA [auth I] Focus chain N [auth B] Focus chain PA [auth L] Interactions & Density Focus chain AA [auth D] Focus chain IA [auth I] Focus chain N [auth B] Focus chain PA [auth L]
HCA (Subject of Investigation/LOI) Query on HCA Download:Ideal Coordinates CCD File SDF format, chain FA [auth H] SDF format, chain LA [auth J] SDF format, chain W [auth C] SDF format, chain I [auth A] MOL2 format, chain FA [auth H] MOL2 format, chain LA [auth J] MOL2 format, chain W [auth C] MOL2 format, chain I [auth A] mmCIF format, chain FA [auth H] mmCIF format, chain LA [auth J] mmCIF format, chain W [auth C] mmCIF format, chain I [auth A]	FA [auth H], I [auth A], LA [auth J], W [auth C]	3-HYDROXY-3-CARBOXY-ADIPIC ACID C₇ H₁₀ O₇ XKJVEVRQMLKSMO-SSDOTTSWSA-N		Interactions Focus chain FA [auth H] Focus chain I [auth A] Focus chain LA [auth J] Focus chain W [auth C] Interactions & Density Focus chain FA [auth H] Focus chain I [auth A] Focus chain LA [auth J] Focus chain W [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain HA [auth H] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain Z [auth C] SDF format, chain SA [auth L] SDF format, chain RA [auth L] SDF format, chain OA [auth J] SDF format, chain M [auth A] SDF format, chain JA [auth I] MOL2 format, chain DA [auth D] MOL2 format, chain HA [auth H] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain Z [auth C] MOL2 format, chain SA [auth L] MOL2 format, chain RA [auth L] MOL2 format, chain OA [auth J] MOL2 format, chain M [auth A] MOL2 format, chain JA [auth I] mmCIF format, chain DA [auth D] mmCIF format, chain HA [auth H] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain Z [auth C] mmCIF format, chain SA [auth L] mmCIF format, chain RA [auth L] mmCIF format, chain OA [auth J] mmCIF format, chain M [auth A] mmCIF format, chain JA [auth I]	DA [auth D] HA [auth H] JA [auth I] M [auth A] OA [auth J] DA [auth D], HA [auth H], JA [auth I], M [auth A], OA [auth J], RA [auth L], SA [auth L], T [auth B], U [auth B], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain DA [auth D] Focus chain HA [auth H] Focus chain JA [auth I] Focus chain M [auth A] Focus chain OA [auth J] Focus chain RA [auth L] Focus chain SA [auth L] Focus chain T [auth B] Focus chain U [auth B] Focus chain Z [auth C] Interactions & Density Focus chain DA [auth D] Focus chain HA [auth H] Focus chain JA [auth I] Focus chain M [auth A] Focus chain OA [auth J] Focus chain RA [auth L] Focus chain SA [auth L] Focus chain T [auth B] Focus chain U [auth B] Focus chain Z [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain L [auth A] SDF format, chain NA [auth J] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain Y [auth C] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain QA [auth L] SDF format, chain P [auth B] SDF format, chain K [auth A] SDF format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain NA [auth J] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth L] MOL2 format, chain P [auth B] MOL2 format, chain K [auth A] MOL2 format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain NA [auth J] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth L] mmCIF format, chain P [auth B] mmCIF format, chain K [auth A] mmCIF format, chain BA [auth D]	BA [auth D] CA [auth D] K [auth A] L [auth A] NA [auth J] BA [auth D], CA [auth D], K [auth A], L [auth A], NA [auth J], O [auth B], P [auth B], Q [auth B], QA [auth L], R [auth B], S [auth B], Y [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain NA [auth J] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth L] Focus chain R [auth B] Focus chain S [auth B] Focus chain Y [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain NA [auth J] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth L] Focus chain R [auth B] Focus chain S [auth B] Focus chain Y [auth C]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain KA [auth I] SDF format, chain V [auth B] SDF format, chain TA [auth L] SDF format, chain EA [auth D] MOL2 format, chain KA [auth I] MOL2 format, chain V [auth B] MOL2 format, chain TA [auth L] MOL2 format, chain EA [auth D] mmCIF format, chain KA [auth I] mmCIF format, chain V [auth B] mmCIF format, chain TA [auth L] mmCIF format, chain EA [auth D]	EA [auth D], KA [auth I], TA [auth L], V [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain KA [auth I] Focus chain TA [auth L] Focus chain V [auth B] Interactions & Density Focus chain EA [auth D] Focus chain KA [auth I] Focus chain TA [auth L] Focus chain V [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.03 Å
R-Value Free: 0.223 (Depositor), 0.221 (DCC)
R-Value Work: 0.204 (Depositor), 0.204 (DCC)
R-Value Observed: 0.205 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.392	α = 90
b = 73.444	β = 104.76
c = 211.253	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
BUSTER	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-06-07

Deposition Author(s):

Wagner, T.

Maslac, N.

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	180544
Swiss National Science Foundation	Switzerland	SNSF 310030_189246
Max Planck Society	Germany	--
German Research Foundation (DFG)	Germany	WA 4053/1-1