1YCF

Oxidized (di-ferric) FprA from Moorella thermoacetica


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

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: 10.1021/bi0473049
  • Primary Citation of Related Structures:  

  • 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 charact ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nitric oxide reductase
A, B, C, D
398Moorella thermoacetica (strain ATCC 39073 / JCM 9320)Mutation(s): 0 
Gene Names: fprA
EC: 1.-.-.-
Find proteins for Q9FDN7 (Moorella thermoacetica (strain ATCC 39073 / JCM 9320))
Go to UniProtKB:  Q9FDN7
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXY
Query on OXY

Download SDF File 
Download CCD File 
A, B, C, D
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FMN
Query on FMN

Download SDF File 
Download CCD File 
A, B, C, D
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
FEO
Query on FEO

Download SDF File 
Download CCD File 
A, B, C, D
MU-OXO-DIIRON
Fe2 O
NPMYUMBHPJGBFA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.217 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 159.670α = 90.00
b = 159.670β = 90.00
c = 276.798γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
CCP4data scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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