6Y1X | pdb_00006y1x

X-ray structure of the radical SAM protein NifB, a key nitrogenase maturating enzyme

PDB DOI: https://doi.org/10.2210/pdb6Y1X/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Methanothrix thermoacetophila PT
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-02-14 Released: 2020-06-17
Deposition Author(s): Sosa-Fajardo, A., Legrand, P., Paya-Tormo, L., Martin, L., Pellicer-Martinez, M.T., Echavarri-Erasun, C., Vernede, X., Rubio, L.M., Nicolet, Y.
Funding Organization(s): French National Research Agency, Spanish Ministry of Science, Innovation, and Universities

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.212 (Depositor), 0.210 (DCC)
R-Value Work:
0.177 (Depositor), 0.178 (DCC)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structural Insights into the Mechanism of the Radical SAM Carbide Synthase NifB, a Key Nitrogenase Cofactor Maturating Enzyme.

Fajardo, A.S., Legrand, P., Paya-Tormo, L.A., Martin, L., Pellicer Marti Nez, M.T., Echavarri-Erasun, C., Vernede, X., Rubio, L.M., Nicolet, Y.

(2020) J Am Chem Soc 142: 11006-11012

PubMed: 32476412 Search on PubMed
DOI: https://doi.org/10.1021/jacs.0c02243
Primary Citation Related Structures:
6Y1X

PubMed Abstract:
Nitrogenase is a key player in the global nitrogen cycle, as it catalyzes the reduction of dinitrogen into ammonia. The active site of the nitrogenase MoFe protein corresponds to a [MoFe ₇S ₉C-( R )-homocitrate] species designated FeMo-cofactor, whose biosynthesis and insertion requires the action of over a dozen maturation proteins provided by the NIF (for NI trogen F ixation) assembly machinery. Among them, the radical SAM protein NifB plays an essential role, concomitantly inserting a carbide ion and coupling two [Fe ₄S ₄] clusters to form a [Fe ₈S ₉C] precursor called NifB-co. Here we report on the X-ray structure of NifB from Methanotrix thermoacetophila at 1.95 Å resolution in a state pending the binding of one [Fe ₄S ₄] cluster substrate. The overall NifB architecture indicates that this enzyme has a single SAM binding site, which at this stage is occupied by cysteine residue 62. The structure reveals a unique ligand binding mode for the K1-cluster involving cysteine residues 29 and 128 in addition to histidine 42 and glutamate 65. The latter, together with cysteine 62, belongs to a loop inserted in the active site, likely protecting the already present [Fe ₄S ₄] clusters. These two residues regulate the sequence of events, controlling SAM dual reactivity and preventing unwanted radical-based chemistry before the K2 [Fe ₄S ₄] cluster substrate is loaded into the protein. The location of the K1-cluster, too far away from the SAM binding site, supports a mechanism in which the K2-cluster is the site of methylation.

Organizational Affiliation

Centro de Biotecnologı́a y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnologı́a Agraria y Alimentaria, Pozuelo de Alarcón, 28223 Madrid, Spain.

Macromolecule Content

Total Structure Weight: 72.55 kDa
Atom Count: 4,519
Modeled Residue Count: 504
Deposited Residue Count: 618
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Radical SAM domain protein	A, B	309	Methanothrix thermoacetophila PT	Mutation(s): 0 Gene Names: Mthe_0422
UniProt
Find proteins for A0B690 (Methanothrix thermoacetophila (strain DSM 6194 / JCM 14653 / NBRC 101360 / PT)) Explore A0B690 Go to UniProtKB: A0B690
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0B690
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 (Subject of Investigation/LOI) Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	C [auth A], D [auth A], K [auth B], L [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain K [auth B] Focus chain L [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	E [auth A], F [auth A], H [auth B], I [auth B], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B]	G [auth A], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.212 (Depositor), 0.210 (DCC)
R-Value Work: 0.177 (Depositor), 0.178 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.18	α = 78.81
b = 48.68	β = 87.73
c = 80.38	γ = 89.94

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
SHELXDE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-06-17

Deposition Author(s):

Pellicer-Martinez, M.T.

Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-17-EURE-0003
French National Research Agency	France	ANR-10-INBS-05-02
French National Research Agency	France	ANR-15-IDEX-02
Spanish Ministry of Science, Innovation, and Universities	Spain	2017-88475-R