Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 130.92 kDa 
• Atom Count: 9,190 
• Modelled Residue Count: 1,165 
• Deposited Residue Count: 1,188 
• Unique protein chains: 1

 1FDY

N-ACETYLNEURAMINATE LYASE IN COMPLEX WITH HYDROXYPYRUVATE

• PDB DOI:  https://doi.org/10.2210/pdb1FDY/pdb

• Classification: LYASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1996-07-08 Released: 1997-10-22 
• Deposition Author(s): Lawrence, M.C., Barbosa, J.A.R.G., Smith, B.J., Hall, N.E., Pilling, P.A., Ooi, H.C., Marcuccio, S.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Work: 0.219 
• R-Value Observed: 0.219 

Literature

Structure and mechanism of a sub-family of enzymes related to N-acetylneuraminate lyase.

Lawrence, M.C., Barbosa, J.A.R.G., Smith, B.J., Hall, N.E., Pilling, P.A., Ooi, H.C., Marcuccio, S.M.

(1997) J Mol Biol 266: 381-399

• PubMed: 9047371 
• DOI: https://doi.org/10.1006/jmbi.1996.0769
• Primary Citation of Related Structures:  
  1FDY, 1FDZ


• PubMed Abstract: 
  

We describe here a sub-family of enzymes related both structurally and functionally to N-acetylneuraminate lyase. Two members of this family (N-acetylneuraminate lyase and dihydrodipicolinate synthase) have known three-dimensional structures and we now proceed to show their structural and functional relationship to two further proteins, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase and D-4-deoxy-5-oxoglucarate dehydratase. These enzymes are all thought to involve intermediate Schiff-base formation with their respective substrates. In order to understand the nature of this intermediate, we have determined the three-dimensional structure of N-acetylneuraminate lyase in complex with hydroxypyruvate (a product analogue) and in complex with one of its products (pyruvate). From these structures we deduce the presence of a closely similar Schiff-base forming motif in all members of the N-acetylneuraminate lyase sub-family. A fifth protein, MosA, is also confirmed to be a member of the sub-family although the involvement of an intermediate Schiff-base in its proposed reaction is unclear.

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Related Citations: 

• The Three-Dimensional Structure of N-Acetylneuraminate Lyase from Escherichia Coli
  Izard, T., Lawrence, M.C., Malby, R.L., Lilley, G.G., Colman, P.M.
  (1994) Structure 2: 361

• High-Level Production and Purification of Escherichia Coli N-Acetylneuraminic Acid Aldolase (Ec 4.1.3.3)
  Lilley, G.G., Von Itzstein, M., Ivanecic, N.
  (1992) Protein Expr Purif 3: 434

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Organizational Affiliation: 

Biomolecular Research Institute, Parkville, Victoria, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-ACETYLNEURAMINATE LYASE	A, B, C, D	297	Escherichia coli	Mutation(s): 0  Gene Names: npl EC: 4.1.3.3
UniProt
Find proteins for P0A6L4 (Escherichia coli (strain K12)) Explore P0A6L4  Go to UniProtKB:  P0A6L4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3PY	E [auth A], F [auth B], G [auth C], H [auth D]	3-HYDROXYPYRUVIC ACID C3 H4 O4 HHDDCCUIIUWNGJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Work: 0.219 
• R-Value Observed: 0.219 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121	α = 90
b = 121	β = 90
c = 196.82	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-10-22 
Deposition Author(s): Lawrence, M.C., Barbosa, J.A.R.G., Smith, B.J., Hall, N.E., Pilling, P.A., Ooi, H.C., Marcuccio, S.M.

Revision History  

• Version 1.0: 1997-10-22
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-06-21
  Changes: Database references, Other
• Version 1.4: 2018-04-04
  Changes: Data collection