4IMC

Crystal Structure of Pasteurella multocida N-Acetyl-D-Neuraminic acid lyase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis for Substrate Specificity and Mechanism of N-Acetyl-d-neuraminic Acid Lyase from Pasteurella multocida.

Huynh, N.Aye, A.Li, Y.Yu, H.Cao, H.Tiwari, V.K.Shin, D.W.Chen, X.Fisher, A.J.

(2013) Biochemistry 52: 8570-8579

  • DOI: 10.1021/bi4011754
  • Primary Citation of Related Structures:  4IMD, 4IME, 4IMF, 4IMG

  • PubMed Abstract: 
  • N-Acetylneuraminate lyases (NALs) or sialic acid aldolases catalyze the reversible aldol cleavage of N-acetylneuraminic acid (Neu5Ac, the most common form of sialic acid) to form pyruvate and N-acetyl-d-mannosamine. Although equilibrium favors sialic ...

    N-Acetylneuraminate lyases (NALs) or sialic acid aldolases catalyze the reversible aldol cleavage of N-acetylneuraminic acid (Neu5Ac, the most common form of sialic acid) to form pyruvate and N-acetyl-d-mannosamine. Although equilibrium favors sialic acid cleavage, these enzymes can be used for high-yield chemoenzymatic synthesis of structurally diverse sialic acids in the presence of excess pyruvate. Engineering these enzymes to synthesize structurally modified natural sialic acids and their non-natural derivatives holds promise in creating novel therapeutic agents. Atomic-resolution structures of these enzymes will greatly assist in guiding mutagenic and modeling studies to engineer enzymes with altered substrate specificity. We report here the crystal structures of wild-type Pasteurella multocida N-acetylneuraminate lyase and its K164A mutant. Like other bacterial lyases, it assembles into a homotetramer with each monomer folding into a classic (β/α)₈ TIM barrel. Two wild-type structures were determined, in the absence of substrates, and trapped in a Schiff base intermediate between Lys164 and pyruvate, respectively. Three structures of the K164A variant were determined: one in the absence of substrates and two binary complexes with N-acetylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc). Both sialic acids bind to the active site in the open-chain ketone form of the monosaccharide. The structures reveal that every hydroxyl group of the linear sugars makes hydrogen bond interactions with the enzyme, and the residues that determine specificity were identified. Additionally, the structures provide some clues for explaining the natural discrimination of sialic acid substrates between the P. multocida and Escherichia coli NALs.


    Organizational Affiliation

    Department of Chemistry, ‡Department of Molecular and Cellular Biology, and §Cell Biology Graduate Program, University of California , One Shields Avenue, Davis, California 95616, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-acetylneuraminate lyase
A, B, C, D
293Pasteurella multocida (strain Pm70)Gene Names: nanA
EC: 4.1.3.3
Find proteins for Q9CKB0 (Pasteurella multocida (strain Pm70))
Go to UniProtKB:  Q9CKB0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 80.946α = 90.00
b = 113.471β = 111.35
c = 82.238γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
SCALAdata scaling
PHASERphasing
MOSFLMdata reduction
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-06
    Type: Initial release
  • Version 1.1: 2013-12-11
    Type: Database references