4D02

The crystallographic structure of Flavorubredoxin from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.755 Å
  • R-Value Work: 0.141 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of Escherichia Coli Flavodiiron Nitric Oxide Reductase.

Romao, C.V.Vicente, J.B.Borges, P.T.Victor, B.L.Lamosa, P.Silva, E.Bandeiras, T.M.Soares, C.M.Carrondo, M.A.Turner, D.Teixeira, M.Frazao, C.

(2016) J.Mol.Biol. 428: 4686

  • DOI: 10.1016/j.jmb.2016.10.008
  • Primary Citation of Related Structures:  5LLD, 5LMC

  • PubMed Abstract: 
  • Flavodiiron proteins (FDPs) are present in organisms from all domains of life and have been described so far to be involved in the detoxification of oxygen or nitric oxide (NO), acting as O2 and/or NO reductases. The Escherichia coli FDP, named flavo ...

    Flavodiiron proteins (FDPs) are present in organisms from all domains of life and have been described so far to be involved in the detoxification of oxygen or nitric oxide (NO), acting as O2 and/or NO reductases. The Escherichia coli FDP, named flavorubredoxin (FlRd), is the most extensively studied FDP. Biochemical and in vivo studies revealed that FlRd is involved in NO detoxification as part of the bacterial defense mechanisms against reactive nitrogen species. E. coli FlRd has a clear preference for NO as a substrate in vitro, exhibiting a very low reactivity toward O2. To contribute to the understanding of the structural features defining this substrate selectivity, we determined the crystallographic structure of E. coli FlRd, both in the isolated and reduced states. The overall tetrameric structure revealed a highly conserved flavodiiron core domain, with a metallo-β-lactamase-like domain containing a diiron center, and a flavodoxin domain with a flavin mononucleotide cofactor. The metal center in the oxidized state has a μ-hydroxo bridge coordinating the two irons, while in the reduced state, this moiety is not detected. Since only the flavodiiron domain was observed in these crystal structures, the structure of the rubredoxin domain was determined by NMR. Tunnels for the substrates were identified, and through molecular dynamics simulations, no differences for O2 or NO permeation were found. The present data represent the first structure for a NO-selective FDP.


    Organizational Affiliation

    Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ANAEROBIC NITRIC OXIDE REDUCTASE FLAVORUBREDOXIN
A
479Escherichia coli (strain K12)Gene Names: norV (flrD, ygaI, ygaJ, ygaK)
Find proteins for Q46877 (Escherichia coli (strain K12))
Go to UniProtKB:  Q46877
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
FMN
Query on FMN

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A
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
O
Query on O

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A
OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.755 Å
  • R-Value Work: 0.141 
  • Space Group: P 6 2 2
Unit Cell:
Length (Å)Angle (°)
a = 149.529α = 90.00
b = 149.529β = 90.00
c = 94.498γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SHELXEmodel building
SHELXCDphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2014-10-22
    Type: Database references
  • Version 1.2: 2017-02-08
    Type: Database references