7ADR | pdb_00007adr

CO bound as bridging ligand at the active site of vanadium nitrogenase VFe protein

• PDB DOI: https://doi.org/10.2210/pdb7ADR/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Azotobacter vinelandii
• Expression System: Azotobacter vinelandii
• Mutation(s): No 


• Deposited: 2020-09-16 Released: 2020-09-30 
• Deposition Author(s): Rohde, M., Grunau, K., Einsle, O.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 
  0.117 (Depositor), 0.117 (DCC) 
• R-Value Work: 
  0.102 (Depositor), 0.102 (DCC) 
• R-Value Observed: 
  0.102 (Depositor) 

Starting Model: experimental

Literature

CO Binding to the FeV Cofactor of CO-Reducing Vanadium Nitrogenase at Atomic Resolution.

Rohde, M., Grunau, K., Einsle, O.

(2020) Angew Chem Int Ed Engl 59: 23626-23630

• PubMed: 32915491 
• DOI: https://doi.org/10.1002/anie.202010790
• Primary Citation Related Structures: 
  7ADR, 7ADY


• PubMed Abstract: 
  

  Nitrogenases reduce N ₂ , the most abundant element in Earth's atmosphere that is otherwise resistant to chemical conversions due to its stable triple bond. Vanadium nitrogenase stands out in that it additionally processes carbon monoxide, a known inhibitor of the reduction of all substrates other than H ⁺ . The reduction of CO leads to the formation of hydrocarbon products, holding the potential for biotechnological applications in analogy to the industrial Fischer-Tropsch process. Here we report the most highly resolved structure of vanadium nitrogenase to date at 1.0 Å resolution, with CO bound to the active site cofactor after catalytic turnover. CO bridges iron ions Fe2 and Fe6, replacing sulfide S2B, in a binding mode that is in line with previous reports on the CO complex of molybdenum nitrogenase. We discuss the structural consequences of continued turnover when CO is removed, which involve the replacement of CO possibly by OH ^- , the movement of Q176 ^D and K361 ^D , the return of sulfide and the emergence of two additional water molecules that are absent in the CO-bound state.

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Organizational Affiliation: 
• Institut für Biochemie, Fakultät für Chemie und Pharmazie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 244.7 kDa 
• Atom Count: 20,071 
• Modeled Residue Count: 2,101 
• Deposited Residue Count: 2,124 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase vanadium-iron protein alpha chain	A, D	474	Azotobacter vinelandii	Mutation(s): 0  Gene Names: vnfD EC: 1.18.6.1
UniProt
Find proteins for P16855 (Azotobacter vinelandii) Explore P16855  Go to UniProtKB:  P16855

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase vanadium-iron protein beta chain	B, E	475	Azotobacter vinelandii	Mutation(s): 0  Gene Names: vnfK EC: 1.18.6.1
UniProt
Find proteins for P16856 (Azotobacter vinelandii) Explore P16856  Go to UniProtKB:  P16856

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase vanadium-iron protein delta chain	C, F	113	Azotobacter vinelandii	Mutation(s): 0  Gene Names: vnfG EC: 1.18.6.1
UniProt
Find proteins for P16857 (Azotobacter vinelandii) Explore P16857  Go to UniProtKB:  P16857

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D6N (Subject of Investigation/LOI)	G [auth A], U [auth D]	FeV C Fe7 N S7 V YNVNIECPQFRAMK-UHFFFAOYSA-N
CLF	M [auth B], Z [auth E]	FE(8)-S(7) CLUSTER Fe8 S7 JKVMXLBGZBULKV-UHFFFAOYSA-N
HCA	H [auth A], V [auth D]	3-HYDROXY-3-CARBOXY-ADIPIC ACID C7 H10 O7 XKJVEVRQMLKSMO-SSDOTTSWSA-N
TRS	K [auth A], L [auth A], Y [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
EDO	AA [auth E], BA [auth E], CA [auth E], DA [auth E], FA [auth F], P [auth B], Q [auth B], R [auth B], T [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
BCT	I [auth A], W [auth D]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
CMO (Subject of Investigation/LOI)	J [auth A], X [auth D]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N
MG	EA [auth F], N [auth B], O [auth B], S [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free:  0.117 (Depositor), 0.117 (DCC) 
• R-Value Work:  0.102 (Depositor), 0.102 (DCC) 
• R-Value Observed: 0.102 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.579	α = 84.11
b = 79.934	β = 72.42
c = 107.223	γ = 75.19

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-09-30 
Deposition Author(s): Rohde, M., Grunau, K., Einsle, O.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	Germany	310656

Revision History  

• Version 1.0: 2020-09-30
  Type: Initial release
  
• Version 1.1: 2020-12-23
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Database references, Refinement description