2WKJ

Crystal structure of the E192N mutant of E. Coli N-acetylneuraminic acid lyase in complex with pyruvate at 1.45A resolution in space group P212121

• PDB DOI: https://doi.org/10.2210/pdb2WKJ/pdb

• Classification: LYASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-06-11 Released: 2009-12-01 
• Deposition Author(s): Campeotto, I., Carr, S.B., Trinh, C.H., Nelson, A.S., Berry, A., Phillips, S.E.V., Pearson, A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.189 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 

Starting Model: experimental

Literature

Structure of an Escherichia coli N-acetyl-D-neuraminic acid lyase mutant, E192N, in complex with pyruvate at 1.45 angstrom resolution.

Campeotto, I., Carr, S.B., Trinh, C.H., Nelson, A.S., Berry, A., Phillips, S.E., Pearson, A.R.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 1088-1090

• PubMed: 19923724 
• DOI: https://doi.org/10.1107/S1744309109037403
• Primary Citation of Related Structures:  
  2WKJ


• PubMed Abstract: 
  

  The structure of a mutant variant of Escherichia coli N-acetyl-d-neuraminic acid lyase (NAL), E192N, in complex with pyruvate has been determined in a new crystal form. It crystallized in space group P2(1)2(1)2(1), with unit-cell parameters a = 78.3, b = 108.5, c = 148.3 angstrom. Pyruvate has been trapped in the active site as a Schiff base with the catalytic lysine (Lys165) without the need for reduction. Unlike the previously published crystallization conditions for the wild-type enzyme, in which a mother-liquor-derived sulfate ion is strongly bound in the catalytic pocket, the low-salt conditions described here will facilitate the determination of further E. coli NAL structures in complex with other activesite ligands.

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Organizational Affiliation: 

Astbury Centre for Structural Molecular Biology, University of Leeds, England.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 134.98 kDa 
• Atom Count: 10,677 
• Modelled Residue Count: 1,192 
• Deposited Residue Count: 1,212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-ACETYLNEURAMINATE LYASE	A, B, C, D	303	Escherichia coli	Mutation(s): 1  EC: 4.1.3.3
UniProt
Find proteins for P0A6L4 (Escherichia coli (strain K12)) Explore P0A6L4  Go to UniProtKB:  P0A6L4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	E [auth A], F [auth C]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PYR	G [auth C], H [auth D]	PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KPI	A, B, C, D	L-PEPTIDE LINKING	C9 H16 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.189 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.329	α = 90
b = 108.049	β = 90
c = 148.309	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-01 
Deposition Author(s): Campeotto, I., Carr, S.B., Trinh, C.H., Nelson, A.S., Berry, A., Phillips, S.E.V., Pearson, A.R.

Revision History  

• Version 1.0: 2009-12-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-12-19
  Changes: Advisory, Data collection, Database references, Derived calculations
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations, Other
• Version 2.1: 2023-11-29
  Changes: Data collection
• Version 2.2: 2023-12-13
  Changes: Refinement description