7JMB

Crystal structure of Nitrogenase iron-molybdenum cofactor biosynthesis enzyme NifB from Methanothermobacter thermautotrophicus with three Fe4S4 clusters

Summary for 7JMB

• Entry DOI: 10.2210/pdb7jmb/pdb
• Descriptor: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifB, IRON/SULFUR CLUSTER (2 entities in total)
• Functional Keywords: nitrogenase, radical sam enzyme, iron-molybdenum cofactor biosynthesis, metal binding protein
• Biological source: Methanothermobacter thermautotrophicus
• Total number of polymer chains: 2
• Total formula weight: 67573.56

Authors

Kang, W.,Rettberg, L.,Ribbe, M.W.,Hu, Y. (deposition date: 2020-07-31, release date: 2020-10-28, Last modification date: 2024-11-20)

Primary citation

Kang, W.,Rettberg, L.A.,Stiebritz, M.T.,Jasniewski, A.J.,Tanifuji, K.,Lee, C.C.,Ribbe, M.W.,Hu, Y.
X-Ray Crystallographic Analysis of NifB with a Full Complement of Clusters: Structural Insights into the Radical SAM-Dependent Carbide Insertion During Nitrogenase Cofactor Assembly.
Angew.Chem.Int.Ed.Engl., 60:2364-2370, 2021

PubMed Abstract: NifB is an essential radical SAM enzyme required for the assembly of an 8Fe core of the nitrogenase cofactor. Herein, we report the X-ray crystal structures of Methanobacterium thermoautotrophicum NifB without (apo MtNifB) and with (holo MtNifB) a full complement of three [Fe S ] clusters. Both apo and holo MtNifB contain a partial TIM barrel core, but unlike apo MtNifB, holo MtNifB is fully assembled and competent in cofactor biosynthesis. The radical SAM (RS)-cluster is coordinated by three Cys, and the adjacent K1- and K2-clusters, representing the precursor to an 8Fe cofactor core, are each coordinated by one His and two Cys. Prediction of substrate channels, combined with in silico docking of SAM in holo MtNifB, suggests the binding of SAM between the RS- and K2-clusters and putative paths for entry of SAM and exit of products of SAM cleavage, thereby providing important mechanistic insights into the radical SAM-dependent carbide insertion concomitant with cofactor core formation.

PubMed: 33035363
DOI: 10.1002/anie.202011367

Experimental method

X-RAY DIFFRACTION (3 Å)