Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 93.82 kDa 
• Atom Count: 7047 
• Modelled Residue Count: 802 
• Deposited Residue Count: 820 
• Unique protein chains: 1

4DIK

Flavo Di-iron protein H90A mutant from Thermotoga maritima

• PDB DOI: 10.2210/pdb4DIK/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-01-31 Released: 2012-10-17 
• Deposition Author(s): Fang, H., Caranto, J.D., Taylor, A.B., Hart, P.J., Kurtz Jr., D.M.

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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 

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

• PubMed: 22990880 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FLAVOPROTEIN	A, B	410	Thermotoga maritima	Mutation(s): 1  Gene Names: TM0755, TM_0755
UniProt
Find proteins for Q9WZL4 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZL4  Go to UniProtKB:  Q9WZL4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FEO	D [auth A], G [auth B]	MU-OXO-DIIRON Fe2 O NPMYUMBHPJGBFA-UHFFFAOYSA-N
CL	C [auth A], E [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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 = 55.219	α = 90
b = 96.007	β = 95.81
c = 90.331	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-01-31 
• Released Date: 2012-10-17 
Deposition Author(s): Fang, H., Caranto, J.D., Taylor, A.B., Hart, P.J., Kurtz Jr., D.M.

Revision History  

• 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