X-ray Structures of Moorella thermoacetica FprA. Novel Diiron Site Structure and Mechanistic Insights into a Scavenging Nitric Oxide Reductase

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

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X-ray crystal structures of Moorella thermoacetica FprA. Novel diiron site structure and mechanistic insights into a scavenging nitric oxide reductase.

Silaghi-Dumitrescu, R.Kurtz Jr, D.M.Ljungdahl, L.G.Lanzilotta, W.N.

(2005) Biochemistry 44: 6492-6501

  • DOI: https://doi.org/10.1021/bi0473049
  • Primary Citation of Related Structures:  
    1YCF, 1YCG, 1YCH

  • PubMed Abstract: 

    Several members of a widespread class of bacterial and archaeal metalloflavoproteins, called FprA, likely function as scavenging nitric oxide reductases (S-NORs). However, the only published X-ray crystal structure of an FprA is for a protein characterized as a rubredoxin:dioxygen oxidoreductase (ROO) from Desulfovibrio gigas. Therefore, the crystal structure of Moorella thermoacetica FprA, which has been established to function as an S-NOR, was solved in three different states: as isolated, reduced, and reduced, NO-reacted. As is the case for D. gigas ROO, the M. thermoacetica FprA contains a solvent-bridged non-heme, non-sulfur diiron site with five-coordinate iron centers bridged by an aspartate, and terminal glutamate, aspartate, and histidine ligands. However, the M. thermoacetica FprA diiron site showed four His ligands, two to each iron, in all three states, whereas the D. gigas ROO diiron site was reported to contain only three His ligands, even though the fourth His residue is conserved. The Fe1-Fe2 distance within the diiron site of M. thermoacetica FprA remained at 3.2-3.4 A with little or no movement of the protein ligands in the three different states and with conservation of the two proximal open coordination sites. Molecular modeling indicated that each open coordination site can accommodate an end-on NO. This relatively rigid and symmetrical diiron site structure is consistent with formation of a diferrous dinitrosyl as the committed catalytic intermediate leading to formation of N(2)O. These results provide new insight into the structural features that fine-tune biological non-heme diiron sites for dioxygen activation vs nitric oxide reduction.

  • Organizational Affiliation

    Department of Chemistry, and Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitric oxide reductase
A, B, C, D
398Moorella thermoaceticaMutation(s): 0 
EC: 1
Find proteins for Q9FDN7 (Moorella thermoacetica (strain ATCC 39073 / JCM 9320))
Explore Q9FDN7 
Go to UniProtKB:  Q9FDN7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FDN7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FMN

Download Ideal Coordinates CCD File 
DA [auth D],
K [auth A],
R [auth B],
X [auth C]
C17 H21 N4 O9 P
Query on FEO

Download Ideal Coordinates CCD File 
BA [auth D],
I [auth A],
P [auth B],
V [auth C]
Fe2 O
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth D]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
AA [auth D],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
S [auth C],
T [auth C],
U [auth C],
Y [auth D],
Z [auth D]
Query on EDO

Download Ideal Coordinates CCD File 
CA [auth D],
J [auth A],
Q [auth B],
W [auth C]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.68α = 90
b = 159.68β = 90
c = 278.136γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-04-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2016-09-21
    Changes: Other
  • Version 1.4: 2018-01-31
    Changes: Experimental preparation