Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 35.43 kDa 
• Atom Count: 2662 
• Modelled Residue Count: 290 
• Deposited Residue Count: 312 
• Unique protein chains: 1

4MLV

Crystal Structure of Bacillus megaterium porphobilinogen deaminase

• PDB DOI: 10.2210/pdb4MLV/pdb

• Classification: TRANSFERASE
• Organism(s): Priestia megaterium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-09-06 Released: 2014-04-02 
• Deposition Author(s): Azim, N., Deery, E., Warren, M.J., Erskine, P., Cooper, J.B., Coker, A., Wood, S.P., Akhtar, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.186 
• R-Value Work: 0.141 
• R-Value Observed: 0.143 

Literature

Structural evidence for the partially oxidized dipyrromethene and dipyrromethanone forms of the cofactor of porphobilinogen deaminase: structures of the Bacillus megaterium enzyme at near-atomic resolution.

Azim, N., Deery, E., Warren, M.J., Wolfenden, B.A., Erskine, P., Cooper, J.B., Coker, A., Wood, S.P., Akhtar, M.

(2014) Acta Crystallogr D Biol Crystallogr 70: 744-751

• PubMed: 24598743 
• DOI: 10.1107/S139900471303294X
• Primary Citation of Related Structures:  
  4MLQ, 4MLV


• PubMed Abstract: 
  

The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses an early step of the tetrapyrrole-biosynthesis pathway in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor, which is covalently linked by a thioether bridge to an invariant cysteine residue (Cys241 in the Bacillus megaterium enzyme). The cofactor is extended during the reaction by the sequential addition of the four substrate molecules, which are released as a linear tetrapyrrole product. Expression in Escherichia coli of a His-tagged form of B. megaterium PBGD has permitted the X-ray analysis of the enzyme from this species at high resolution, showing that the cofactor becomes progressively oxidized to the dipyrromethene and dipyrromethanone forms. In previously solved PBGD structures, the oxidized cofactor is in the dipyromethenone form, in which both pyrrole rings are approximately coplanar. In contrast, the oxidized cofactor in the B. megaterium enzyme appears to be in the dipyrromethanone form, in which the C atom at the bridging α-position of the outer pyrrole ring is very clearly in a tetrahedral configuration. It is suggested that the pink colour of the freshly purified protein is owing to the presence of the dipyrromethene form of the cofactor which, in the structure reported here, adopts the same conformation as the fully reduced dipyrromethane form.

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Organizational Affiliation: 

School of Biological Sciences, University of Punjab, New Campus, Lahore-54590, Pakistan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Porphobilinogen deaminase	A	312	Priestia megaterium	Mutation(s): 0  Gene Names: hemC, C3744_10255 EC: 2.5.1.61
UniProt
Find proteins for Q8GCA8 (Priestia megaterium) Explore Q8GCA8  Go to UniProtKB:  Q8GCA8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
29P	C [auth A]	3-[(5S)-5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-2-oxo-2,5-dihydro-1H-pyrrol-3-yl]propanoic acid C20 H24 N2 O9 DHEOBTWDCMSDOQ-HNNXBMFYSA-N
DPM	B [auth A]	3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid C20 H24 N2 O8 LCAXMKQKEYTFDM-UHFFFAOYSA-N
ACY	D [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.186 
• R-Value Work: 0.141 
• R-Value Observed: 0.143 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.32	α = 90
b = 65.78	β = 90
c = 97.21	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-09-06 
• Released Date: 2014-04-02 
Deposition Author(s): Azim, N., Deery, E., Warren, M.J., Erskine, P., Cooper, J.B., Coker, A., Wood, S.P., Akhtar, M.

Revision History  

• Version 1.0: 2014-04-02
  Type: Initial release