1WCQ

Mutagenesis of the Nucleophilic Tyrosine in a Bacterial Sialidase to Phenylalanine.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Two Nucleophilic Mutants of the Micromonospora Viridifaciens Sialidase Operate with Retention of Configuration by Two Different Mechanisms.

Watson, J.N.Newstead, S.Narine, A.A.Taylor, G.Bennet, A.J.

(2005) Chembiochem 6: 1439

  • DOI: 10.1002/cbic.200500114

  • PubMed Abstract: 
  • Mutants of the Micromonospora viridifaciens sialidase, Y370E and Y370F, are catalytically active retaining enzymes that operate by different mechanisms. Previous substitutions with smaller amino acids, including Y370D, yielded inverting sialidases. A ...

    Mutants of the Micromonospora viridifaciens sialidase, Y370E and Y370F, are catalytically active retaining enzymes that operate by different mechanisms. Previous substitutions with smaller amino acids, including Y370D, yielded inverting sialidases. At least one water molecule can fit into the active-site cavity of this mutant and act as a nucleophile from the face opposite the leaving group (Biochemistry 2003, 42, 12 682). Thus, addition of a CH(2) unit (Asp versus Glu) changes the mechanism from inversion back to retention of configuration. Based on Brønsted beta(lg) values, it is proposed that the Y370E mutant reacts by a double-displacement mechanism (beta(lg) on k(cat)/K(m) -0.36+/-0.04) with Glu370 acting as the nucleophile. However, the Y370F mutant (beta(lg) on k(cat)/K(m) -0.79+/-0.12) reacts via a dissociative transition state. The crystal structure of the Y370F mutant complexed with 2-deoxy-2,3-dehydro-N-acetylneuraminic acid shows no significant active-site perturbation relative to the wild-type enzyme.


    Organizational Affiliation

    Department of Chemistry, Simon Fraser University, University Drive, Burnaby, BC, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SIALIDASE
A, B, C
601Micromonospora viridifaciensGene Names: nedA
EC: 3.2.1.18
Find proteins for Q02834 (Micromonospora viridifaciens)
Go to UniProtKB:  Q02834
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DAN
Query on DAN

Download SDF File 
Download CCD File 
A, B, C
2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
C11 H17 N O8
JINJZWSZQKHCIP-UFGQHTETSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DANKi: 550 nM BINDINGMOAD
DANKi: 550 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.175 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 143.258α = 90.00
b = 143.258β = 90.00
c = 160.250γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance