Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34546.70 
• Atom Count: 2298 
• Residue Count: 313 
• Unique protein chains: 1

1AH5

REDUCED FORM SELENOMETHIONINE-LABELLED HYDROXYMETHYLBILANE SYNTHASE DETERMINED BY MAD

• DOI: 10.2210/pdb1AH5/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli


• Deposited: 1997-04-13 Released: 1997-10-15 
• Deposition Author(s): Helliwell, J.R., Nieh, Y.P., Harrop, S.J., Cassetta, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.235 
• R-Value Work: 0.168 

Literature

Determination of the structure of seleno-methionine-labelled hydroxymethylbilane synthase in its active form by multi-wavelength anomalous dispersion.

Hadener, A., Matzinger, P.K., Battersby, A.R., McSweeney, S., Thompson, A.W., Hammersley, A.P., Harrop, S.J., Cassetta, A., Deacon, A., Hunter, W.N., Nieh, Y.P., Raftery, J., Hunter, N., Helliwell, J.R.

(1999) Acta Crystallogr.,Sect.D 55: 631-643

• PubMed: 10089459 


• PubMed Abstract: 
  

The enzyme hydroxymethylbilane synthase (HMBS, E.C. 4.3.1.8) catalyzes the conversion of porphobilinogen into hydroxymethylbilane, a key intermediate for the biosynthesis of heme, chlorophylls, vitamin B12 and related macrocycles. The enzyme is found in all organisms, except viruses. The crystal structure of the selenomethionine-labelled enzyme ([SeMet]HMBS) from Escherichia coli has been solved by the multi-wavelength anomalous dispersion (MAD) experimental method using the Daresbury SRS station 9.5. In addition, [SeMet]HMBS has been studied by MAD at the Grenoble ESRF MAD beamline BM14 (BL19) and this work is described especially with respect to the use of the ESRF CCD detector. The structure at ambient temperature has been refined, the R factor being 16.8% at 2. 4 A resolution. The dipyrromethane cofactor of the enzyme is preserved in its reduced form in the crystal and its geometrical shape is in full agreement with the crystal structures of authentic dipyrromethanes. Proximal to the reactive C atom of the reduced cofactor, spherical density is seen consistent with there being a water molecule ideally placed to take part in the final step of the enzyme reaction cycle. Intriguingly, the loop with residues 47-58 is not ordered in the structure of this form of the enzyme, which carries no substrate. Direct experimental study of the active enzyme is now feasible using time-resolved Laue diffraction and freeze-trapping, building on the structural work described here as the foundation.

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Organizational Affiliation: 

Department of Chemistry, University of Basle, Switzerland. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HYDROXYMETHYLBILANE SYNTHASE	A	313	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: hemC (popE) EC: 2.5.1.61
Find proteins for P06983 (Escherichia coli (strain K12)) Go to UniProtKB:  P06983

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
DPM	A	3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid DIPYRROMETHANE COFACTOR C20 H24 N2 O8 LCAXMKQKEYTFDM-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.235 
• R-Value Work: 0.168 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 88.470	α = 90.00
b = 76.150	β = 90.00
c = 50.790	γ = 90.00

Software Package:

Software Name	Purpose
MOSFLM	data reduction
ROTAVATA)	data scaling
CCP4	data scaling
MLPHARE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-04-13 
• Released Date: 1997-10-15 
• Deposition Author(s): Helliwell, J.R., Nieh, Y.P., Harrop, S.J., Cassetta, A.

Revision History 

• Version 1.0: 1997-10-15
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2013-09-18
  Type: Non-polymer description