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


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 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-ACETYLNEURAMINATE LYASEA, B, C, D303Escherichia coliMutation(s): 1 
EC: 4.1.3.3
UniProt
Find proteins for P0A6L4 (Escherichia coli (strain K12))
Explore P0A6L4 
Go to UniProtKB:  P0A6L4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6L4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
E [auth A],
F [auth C]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
PYR
Query on PYR

Download Ideal Coordinates CCD File 
G [auth C],
H [auth D]
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KPI
Query on KPI
A, B, C, D L-PEPTIDE LINKINGC9 H16 N2 O4LYS
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 = 78.329α = 90
b = 108.049β = 90
c = 148.309γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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