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: 61.18 kDa 
• Atom Count: 4251 
• Modelled Residue Count: 514 
• Deposited Residue Count: 534 
• Unique protein chains: 1

1RQL

Crystal Structure of Phosponoacetaldehyde Hydrolase Complexed with Magnesium and the Inhibitor Vinyl Sulfonate

• PDB DOI: 10.2210/pdb1RQL/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus cereus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-12-05 Released: 2004-04-20 
• Deposition Author(s): Morais, M.C., Zhang, G., Zhang, W., Olsen, D.B., Dunaway-Mariano, D., Allen, K.N.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.282 
• R-Value Work: 0.227 
• R-Value Observed: 0.227 

Literature

X-ray crystallographic and site-directed mutagenesis analysis of the mechanism of Schiff-base formation in phosphonoacetaldehyde hydrolase catalysis

Morais, M.C., Zhang, G., Zhang, W., Olsen, D.B., Dunaway-Mariano, D., Allen, K.N.

(2004) J Biol Chem 279: 9353-9361

• PubMed: 14670958 
• DOI: 10.1074/jbc.M312345200
• Primary Citation of Related Structures:  
  1RQL, 1RQN


• PubMed Abstract: 
  

Phosphonoacetaldehyde hydrolase (phosphonatase) catalyzes the hydrolytic P-C bond cleavage of phosphonoacetaldehyde (Pald) to form orthophosphate and acetaldehyde. The reaction proceeds via a Schiff-base intermediate formed between Lys-53 and the Pald carbonyl. The x-ray crystal structures of the wild-type phosphonatase complexed with Mg(II) alone or with Mg(II) plus vinylsulfonate (a phosphonoethylenamine analog) were determined to 2.8 and 2.4 A, respectively. These structures were used to determine the identity and positions of active site residues surrounding the Lys-53 ammonium group and the Pald carbonyl. These include Cys-22, His-56, Tyr-128, and Met-49. Site-directed mutagenesis was then employed to determine whether or not these groups participate in catalysis. Based on rate contributions, Tyr-128 and Cys-22 were eliminated as potential catalytic groups. The Lys-53 epsilon-amino group, positioned for reaction with the Pald carbonyl, forms a hydrogen bond with water 120. Water 120 is also within hydrogen bond distance of an imidazole nitrogen of His-56 and the sulfur atom of Met-49. Kinetic constants for mutants indicated that His-56 (1000-fold reduction in k(cat)/K(m) upon Ala substitution) and Met-49 (17,000-fold reduction in k(cat)/K(m) upon Leu substitution) function in catalysis of Schiff-base formation. Based on these results, it is proposed that a network of hydrogen bonds among Lys-53, water 120, His-56, and Met-49 facilitate proton transfer from Lys-53 to the carbinolamine intermediate. Comparison of the vinylsulfonate complex versus unliganded structures indicated that association of the cap and core domains is essential for the positioning of the Lys-53 for attack at the Pald carbonyl and that substrate binding at the core domain stabilizes cap domain binding.

---

Organizational Affiliation: 

Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts 02118-2394, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphonoacetaldehyde Hydrolase	A, B	267	Bacillus cereus	Mutation(s): 0  Gene Names: phnX EC: 3.11.1.1
UniProt
Find proteins for O31156 (Bacillus cereus) Explore O31156  Go to UniProtKB:  O31156

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VSO	E [auth B]	VINYLSULPHONIC ACID C2 H4 O3 S NLVXSWCKKBEXTG-UHFFFAOYSA-N
MG	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
VSO	Binding MOAD:  1RQL	Ki: 1.79e+6 (nM) from 1 assay(s)
	PDBBind:  1RQL	Ki: 1.79e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.282 
• R-Value Work: 0.227 
• R-Value Observed: 0.227 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 209.97	α = 90
b = 45.27	β = 104.92
c = 64.63	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-12-05 
• Released Date: 2004-04-20 
Deposition Author(s): Morais, M.C., Zhang, G., Zhang, W., Olsen, D.B., Dunaway-Mariano, D., Allen, K.N.

Revision History  

• Version 1.0: 2004-04-20
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance