5OV6

Bacillus megaterium porphobilinogen deaminase D82N mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural studies of domain movement in active-site mutants of porphobilinogen deaminase from Bacillus megaterium.

Guo, J.Erskine, P.Coker, A.R.Wood, S.P.Cooper, J.B.

(2017) Acta Crystallogr F Struct Biol Commun 73: 612-620

  • DOI: 10.1107/S2053230X17015436
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The enzyme porphobilinogen deaminase (PBGD) is one of the key enzymes in tetrapyrrole biosynthesis. It catalyses the formation of a linear tetrapyrrole from four molecules of the substrate porphobilinogen (PBG). It has a dipyrromethane cofactor (DPM) ...

    The enzyme porphobilinogen deaminase (PBGD) is one of the key enzymes in tetrapyrrole biosynthesis. It catalyses the formation of a linear tetrapyrrole from four molecules of the substrate porphobilinogen (PBG). It has a dipyrromethane cofactor (DPM) in the active site which is covalently linked to a conserved cysteine residue through a thioether bridge. The substrate molecules are linked to the cofactor in a stepwise head-to-tail manner during the reaction, which is catalysed by a conserved aspartate residue: Asp82 in the B. megaterium enzyme. Three mutations have been made affecting Asp82 (D82A, D82E and D82N) and their crystal structures have been determined at resolutions of 2.7, 1.8 and 1.9 Å, respectively. These structures reveal that whilst the D82E mutant possesses the DPM cofactor, in the D82N and D82A mutants the cofactor is likely to be missing, incompletely assembled or disordered. Comparison of the mutant PBGD structures with that of the wild-type enzyme shows that there are significant domain movements and suggests that the enzyme adopts `open' and `closed' conformations, potentially in response to substrate binding.


    Organizational Affiliation

    Division of Medicine, University College London, Gower Street, London WC1E 6BT, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Porphobilinogen deaminase
A
310Bacillus megateriumMutation(s): 1 
Gene Names: hemC
EC: 2.5.1.61
Find proteins for Q8GCA8 (Bacillus megaterium)
Go to UniProtKB:  Q8GCA8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AWQ
Query on AWQ

Download SDF File 
Download CCD File 
A
3-[4-(2-hydroxy-2-oxoethyl)-2,5-dimethyl-1~{H}-pyrrol-3-yl]propanoic acid
C11 H15 N O4
KJONRYZJTCYQHI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.990α = 90.00
b = 62.690β = 90.00
c = 91.260γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
Cootmodel building
REFMACrefinement
xia2data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-09-06
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Database references