1FDY

N-ACETYLNEURAMINATE LYASE IN COMPLEX WITH HYDROXYPYRUVATE


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

  • DOI: 10.1006/jmbi.1996.0769
  • Primary Citation of Related Structures:  1FDZ
  • Also Cited By: 1HL2

  • 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 n ...

    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.


    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


    Organizational Affiliation

    Biomolecular Research Institute, Parkville, Victoria, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-ACETYLNEURAMINATE LYASE
A, B, C, D
297Escherichia coli (strain K12)Gene Names: nanA (npl)
EC: 4.1.3.3
Find proteins for P0A6L4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6L4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3PY
Query on 3PY

Download SDF File 
Download CCD File 
A, B, C, D
3-HYDROXYPYRUVIC ACID
C3 H4 O4
HHDDCCUIIUWNGJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Work: 0.219 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 121.000α = 90.00
b = 121.000β = 90.00
c = 196.820γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
SCALEPACKdata scaling
X-PLORphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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