4TKU | pdb_00004tku

Reactivated Nitrogenase MoFe-protein from A. vinelandii

PDB DOI: https://doi.org/10.2210/pdb4TKU/pdb

Classification: OXIDOREDUCTASE
Organism(s): Azotobacter vinelandii
Mutation(s): No

Deposited: 2014-05-27 Released: 2014-10-01
Deposition Author(s): Spatzal, T., Perez, K., Einsle, O., Howard, J.B., Rees, D.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free:
0.142 (Depositor), 0.133 (DCC)
R-Value Work:
0.132 (Depositor), 0.132 (DCC)
R-Value Observed:
0.132 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Ligand binding to the FeMo-cofactor: structures of CO-bound and reactivated nitrogenase.

Spatzal, T., Perez, K.A., Einsle, O., Howard, J.B., Rees, D.C.

(2014) Science 345: 1620-1623

PubMed: 25258081 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.1256679
Primary Citation Related Structures:
4TKU, 4TKV

PubMed Abstract:
The mechanism of nitrogenase remains enigmatic, with a major unresolved issue concerning how inhibitors and substrates bind to the active site. We report a crystal structure of carbon monoxide (CO)-inhibited nitrogenase molybdenum-iron (MoFe)-protein at 1.50 angstrom resolution, which reveals a CO molecule bridging Fe2 and Fe6 of the FeMo-cofactor. The μ2 binding geometry is achieved by replacing a belt-sulfur atom (S2B) and highlights the generation of a reactive iron species uncovered by the displacement of sulfur. The CO inhibition is fully reversible as established by regain of enzyme activity and reappearance of S2B in the 1.43 angstrom resolution structure of the reactivated enzyme. The substantial and reversible reorganization of the FeMo-cofactor accompanying CO binding was unanticipated and provides insights into a catalytically competent state of nitrogenase.

Organizational Affiliation

Howard Hughes Medical Institute and Division of Chemistry and Chemical Engineering, MailCode 114-96, California Institute of Technology, Pasadena, CA 91125, USA. spatzal@caltech.edu dcrees@caltech.edu.

Macromolecule Content

Total Structure Weight: 233.86 kDa
Atom Count: 17,913
Modeled Residue Count: 1,998
Deposited Residue Count: 2,030
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase molybdenum-iron protein alpha chain	A, C	492	Azotobacter vinelandii	Mutation(s): 0 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	523	Azotobacter vinelandii	Mutation(s): 0 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 Query on ICS Download:Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain F [auth A] MOL2 format, chain O [auth C] MOL2 format, chain F [auth A] mmCIF format, chain O [auth C] mmCIF format, chain F [auth A]	F [auth A], O [auth C]	iron-sulfur-molybdenum cluster with interstitial carbon C Fe₇ Mo S₉ DDQFAOMIVKLFON-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain O [auth C] Interactions & Density Focus chain F [auth A] Focus chain O [auth C]
CLF Query on CLF Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain I [auth B] MOL2 format, chain R [auth D] MOL2 format, chain I [auth B] mmCIF format, chain R [auth D] mmCIF format, chain I [auth B]	I [auth B], R [auth D]	FE(8)-S(7) CLUSTER Fe₈ S₇ JKVMXLBGZBULKV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain R [auth D] Interactions & Density Focus chain I [auth B] Focus chain R [auth D]
HCA Query on HCA Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain E [auth A] MOL2 format, chain N [auth C] MOL2 format, chain E [auth A] mmCIF format, chain N [auth C] mmCIF format, chain E [auth A]	E [auth A], N [auth C]	3-HYDROXY-3-CARBOXY-ADIPIC ACID C₇ H₁₀ O₇ XKJVEVRQMLKSMO-SSDOTTSWSA-N		Interactions Focus chain E [auth A] Focus chain N [auth C] Interactions & Density Focus chain E [auth A] Focus chain N [auth C]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain P [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A] J [auth B] K [auth B] L [auth B] P [auth C] G [auth A], J [auth B], K [auth B], L [auth B], P [auth C], S [auth D], T [auth D], U [auth D]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D]
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain M [auth B] MOL2 format, chain V [auth D] MOL2 format, chain M [auth B] mmCIF format, chain V [auth D] mmCIF format, chain M [auth B]	M [auth B], V [auth D]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain V [auth D] Interactions & Density Focus chain M [auth B] Focus chain V [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain H [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain H [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain H [auth A]	H [auth A], Q [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain Q [auth C] Interactions & Density Focus chain H [auth A] Focus chain Q [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.142 (Depositor), 0.133 (DCC)
R-Value Work: 0.132 (Depositor), 0.132 (DCC)
R-Value Observed: 0.132 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.941	α = 90
b = 130.785	β = 110.58
c = 107.005	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-10-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-10-01
Type: Initial release
Version 1.1: 2014-10-15
Changes: Database references
Version 1.2: 2023-12-27
Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy