1W8N

Contribution of the Active Site Aspartic Acid to Catalysis in the Bacterial Neuraminidase from Micromonospora viridifaciens.

• PDB DOI: https://doi.org/10.2210/pdb1W8N/pdb

• Classification: HYDROLASE
• Organism(s): Micromonospora viridifaciens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-09-24 Released: 2004-09-30 
• Deposition Author(s): Newstead, S., Watson, J.N., Dookhun, V., Bennet, A.J., Taylor, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.219 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Starting Model: experimental

Literature

Contribution of the Active Site Aspartic Acid to Catalysis in the Bacterial Neuraminidase from Micromonospora Viridifaciens

Watson, J.N., Newstead, S., Dookhun, V., Taylor, G., Bennet, A.J.

(2004) FEBS Lett 577: 265

• PubMed: 15527797 
• DOI: https://doi.org/10.1016/j.febslet.2004.10.016
• Primary Citation of Related Structures:  
  1W8N, 1W8O


• PubMed Abstract: 
  

  A recombinant D92G mutant sialidase from Micromonospora viridifaciens has been cloned, expressed and purified. Kinetic studies reveal that the replacement of the conserved aspartic acid with glycine results in a catalytically competent retaining sialidase that possesses significant activity against activated substrates. The contribution of this aspartate residue to the free energy of hydrolysis for natural substrates is greater than 19 kJ/mol. The three dimensional structure of the D92G mutant shows that the removal of aspartic acid 92 causes no significant re-arrangement of the active site, and that an ordered water molecule substitutes for the carboxylate group of D92.

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Organizational Affiliation: 

Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, Canada V5A 1S6.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 64.73 kDa 
• Atom Count: 5,105 
• Modelled Residue Count: 601 
• Deposited Residue Count: 601 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BACTERIAL SIALIDASE	A	601	Micromonospora viridifaciens	Mutation(s): 1  EC: 3.2.1.18
UniProt
Find proteins for Q02834 (Micromonospora viridifaciens) Explore Q02834  Go to UniProtKB:  Q02834

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DAN	C [auth A]	2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID C11 H17 N O8 JINJZWSZQKHCIP-UFGQHTETSA-N
GAL	B [auth A]	beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.219 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.602	α = 90
b = 111.608	β = 90
c = 143.865	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-30 
Deposition Author(s): Newstead, S., Watson, J.N., Dookhun, V., Bennet, A.J., Taylor, G.

Revision History  

• Version 1.0: 2004-09-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-07-05
  Changes: Data collection
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.5: 2024-11-06
  Changes: Structure summary