1FDZ

N-ACETYLNEURAMINATE LYASE IN COMPLEX WITH PYRUVATE VIA BOROHYDRIDE REDUCTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.4 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
  • Structures With Same Primary Citation

  • 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 LYASEA, B, C, D297Escherichia coliMutation(s): 0 
Gene Names: npl
EC: 4.1.3.3
Find proteins for P0A6L4 (Escherichia coli (strain K12))
Explore P0A6L4 
Go to UniProtKB:  P0A6L4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PYR
Query on PYR

Download CCD File 
A, B, C, D
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121α = 90
b = 121β = 90
c = 196.12γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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