6NZJ

Structural Analysis of a Nitrogenase Iron Protein from Methanosarcina acetivorans: Implications for CO2 Capture by a Surface-Exposed [Fe4S4] Cluster


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural Analysis of a Nitrogenase Iron Protein from Methanosarcina acetivorans: Implications for CO 2 Capture by a Surface-Exposed [Fe 4 S 4 ] Cluster.

Rettberg, L.A.Kang, W.Stiebritz, M.T.Hiller, C.J.Lee, C.C.Liedtke, J.Ribbe, M.W.Hu, Y.

(2019) mBio 10

  • DOI: 10.1128/mBio.01497-19
  • Primary Citation of Related Structures:  
    6NZJ

  • PubMed Abstract: 
  • Nitrogenase iron (Fe) proteins reduce CO 2 to CO and/or hydrocarbons under ambient conditions. Here, we report a 2.4-Å crystal structure of the Fe protein from Methanosarcina acetivorans ( Ma NifH), which is generated in the presence of a reductant, dithionite, and an alternative CO 2 source, bicarbonate ...

    Nitrogenase iron (Fe) proteins reduce CO 2 to CO and/or hydrocarbons under ambient conditions. Here, we report a 2.4-Å crystal structure of the Fe protein from Methanosarcina acetivorans ( Ma NifH), which is generated in the presence of a reductant, dithionite, and an alternative CO 2 source, bicarbonate. Structural analysis of this methanogen Fe protein species suggests that CO 2 is possibly captured in an unactivated, linear conformation near the [Fe 4 S 4 ] cluster of Ma NifH by a conserved arginine (Arg) pair in a concerted and, possibly, asymmetric manner. Density functional theory calculations and mutational analyses provide further support for the capture of CO 2 on Ma NifH while suggesting a possible role of Arg in the initial coordination of CO 2 via hydrogen bonding and electrostatic interactions. These results provide a useful framework for further mechanistic investigations of CO 2 activation by a surface-exposed [Fe 4 S 4 ] cluster, which may facilitate future development of FeS catalysts for ambient conversion of CO 2 into valuable chemical commodities. IMPORTANCE This work reports the crystal structure of a previously uncharacterized Fe protein from a methanogenic organism, which provides important insights into the structural properties of the less-characterized, yet highly interesting archaeal nitrogenase enzymes. Moreover, the structure-derived implications for CO 2 capture by a surface-exposed [Fe 4 S 4 ] cluster point to the possibility of developing novel strategies for CO 2 sequestration while providing the initial insights into the unique mechanism of FeS-based CO 2 activation.


    Organizational Affiliation

    Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA mribbe@uci.edu yilinh@uci.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nitrogenase iron proteinA, B273Methanosarcina acetivorans C2AMutation(s): 0 
Gene Names: nifHMA_3895
EC: 1.18.6.1
UniProt
Find proteins for Q8TJ93 (Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A))
Explore Q8TJ93 
Go to UniProtKB:  Q8TJ93
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TJ93
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
C [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.169α = 90
b = 96.169β = 90
c = 320.244γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE-1651398

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-24
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.3: 2020-04-29
    Changes: Database references
  • Version 1.4: 2020-09-30
    Changes: Database references, Derived calculations