4DIK

Flavo Di-iron protein H90A mutant from Thermotoga maritima


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Histidine ligand variants of a flavo-diiron protein: effects on structure and activities.

Fang, H.Caranto, J.D.Mendoza, R.Taylor, A.B.Hart, P.J.Kurtz, D.M.

(2012) J Biol Inorg Chem 17: 1231-1239

  • DOI: 10.1007/s00775-012-0938-4
  • Primary Citation of Related Structures:  
    4DIK, 4DIL

  • PubMed Abstract: 
  • Flavo-diiron proteins (FDPs) contain non-heme diiron and proximal flavin mononucleotide (FMN) active sites and function as terminal components of a nitric oxide reductase (NOR) and/or a four-electron dioxygen reductase (O(2)R). While most FDPs show similar structural, spectroscopic, and redox properties, O(2)R and NOR activities vary significantly among FDPs ...

    Flavo-diiron proteins (FDPs) contain non-heme diiron and proximal flavin mononucleotide (FMN) active sites and function as terminal components of a nitric oxide reductase (NOR) and/or a four-electron dioxygen reductase (O(2)R). While most FDPs show similar structural, spectroscopic, and redox properties, O(2)R and NOR activities vary significantly among FDPs. A potential source of this variability is the iron ligation status of a conserved His residue that provides an iron ligand in all known FDP structures but one, where this His residue is rotated away from iron and replaced by a solvent ligand. In order to test the effect of this His ligation status, we changed this ligating His residue (H90) in Thermotoga maritima (Tm) FDP to either Asn or Ala. The wild-type Tm FDP shows significantly higher O(2)R than NOR activity. Single crystal X-ray crystallography revealed a remarkably conserved diiron site structure in the H90N and -A variants, differing mainly by either Asn or solvent coordination, respectively, in place of H90. The steady-state activities were minimally affected by the H90 substitutions, remaining significantly higher for O(2)R versus NOR. The pre-steady-state kinetics of the fully reduced FDP with O(2) were also minimally affected by the H90 substitutions. The results indicate that the coordination status of this His ligand does not significantly modulate the O(2)R or NOR activities, and that FDPs can retain these activities when the individual iron centers are differentiated by His ligand substitution. This differentiation may have implications for the O(2)R and NOR mechanisms of FDPs.


    Organizational Affiliation

    Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FLAVOPROTEINA, B410Thermotoga maritimaMutation(s): 1 
Gene Names: TM0755TM_0755
UniProt
Find proteins for Q9WZL4 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WZL4 
Go to UniProtKB:  Q9WZL4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WZL4
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.219α = 90
b = 96.007β = 95.81
c = 90.331γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2013-01-02
    Changes: Database references
  • Version 1.2: 2018-01-24
    Changes: Structure summary