5KOH

Nitrogenase MoFeP from Gluconacetobacter diazotrophicus in dithionite reduced state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.130 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Tyrosine-Coordinated P-Cluster in G. diazotrophicus Nitrogenase: Evidence for the Importance of O-Based Ligands in Conformationally Gated Electron Transfer.

Owens, C.P.Katz, F.E.Carter, C.H.Oswald, V.F.Tezcan, F.A.

(2016) J Am Chem Soc 138: 10124-10127

  • DOI: 10.1021/jacs.6b06783
  • Primary Citation of Related Structures:  
    5KOJ, 5KOH

  • PubMed Abstract: 
  • The P-cluster is a unique iron-sulfur center that likely functions as a dynamic electron (e(-)) relay site between the Fe-protein and the catalytic FeMo-cofactor in nitrogenase. The P-cluster has been shown to undergo large conformational changes upon 2-e(-) oxidation which entail the coordination of two of the Fe centers to a Ser side chain and a backbone amide N, respectively ...

    The P-cluster is a unique iron-sulfur center that likely functions as a dynamic electron (e(-)) relay site between the Fe-protein and the catalytic FeMo-cofactor in nitrogenase. The P-cluster has been shown to undergo large conformational changes upon 2-e(-) oxidation which entail the coordination of two of the Fe centers to a Ser side chain and a backbone amide N, respectively. Yet, how and if this 2-e(-) oxidized state (P(OX)) is involved in catalysis by nitrogenase is not well established. Here, we present the crystal structures of reduced and oxidized MoFe-protein (MoFeP) from Gluconacetobacter diazotrophicus (Gd), which natively possesses an Ala residue in the position of the Ser ligand to the P-cluster. While reduced Gd-MoFeP is structurally identical to previously characterized counterparts around the FeMo-cofactor, oxidized Gd-MoFeP features an unusual Tyr coordination to its P-cluster along with ligation by a backbone amide nitrogen. EPR analysis of the oxidized Gd-MoFeP P-cluster confirmed that it is a 2-e(-) oxidized, integer-spin species. Importantly, we have found that the sequence positions corresponding to the Ser and Tyr ligands are almost completely covariant among Group I nitrogenases. These findings strongly support the possibility that the P(OX) state is functionally relevant in nitrogenase catalysis and that a hard, O-based anionic ligand serves to stabilize this state in a switchable fashion.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0356, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nitrogenase protein alpha chainA, C499Gluconacetobacter diazotrophicus PA1 5Mutation(s): 0 
Gene Names: nifDGDI0437Gdia_1569
EC: 1.18.6.1
UniProt
Find proteins for A9H5W5 (Gluconacetobacter diazotrophicus (strain ATCC 49037 / DSM 5601 / CCUG 37298 / CIP 103539 / LMG 7603 / PAl5))
Explore A9H5W5 
Go to UniProtKB:  A9H5W5
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nitrogenase FeMo beta subunit protein NifKB, D511Gluconacetobacter diazotrophicus PA1 5Mutation(s): 0 
Gene Names: nifKGDI0438Gdia_1568
EC: 1.18.6.1
UniProt
Find proteins for A9H5W8 (Gluconacetobacter diazotrophicus (strain ATCC 49037 / DSM 5601 / CCUG 37298 / CIP 103539 / LMG 7603 / PAl5))
Explore A9H5W8 
Go to UniProtKB:  A9H5W8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ICS
Query on ICS

Download Ideal Coordinates CCD File 
F [auth A], M [auth C]iron-sulfur-molybdenum cluster with interstitial carbon
C Fe7 Mo S9
DDQFAOMIVKLFON-UHFFFAOYSA-N
 Ligand Interaction
CLF (Subject of Investigation/LOI)
Query on CLF

Download Ideal Coordinates CCD File 
I [auth A], O [auth C]FE(8)-S(7) CLUSTER
Fe8 S7
JKVMXLBGZBULKV-DHHOTQGYAO
 Ligand Interaction
HCA (Subject of Investigation/LOI)
Query on HCA

Download Ideal Coordinates CCD File 
E [auth A], L [auth C]3-HYDROXY-3-CARBOXY-ADIPIC ACID
C7 H10 O7
XKJVEVRQMLKSMO-SSDOTTSWSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
N [auth C](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
MRD
Query on MRD

Download Ideal Coordinates CCD File 
G [auth A], H [auth A](4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
J [auth B], K [auth B]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.130 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 202.598α = 90
b = 202.598β = 90
c = 132.567γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
XDSdata scaling
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM099813
Frasch FoundationUnited States735-HF12
NIFAUnited States2015-67012-22895

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2017-08-23
    Changes: Data collection, Derived calculations
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Refinement description
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence, Derived calculations