1HL2

Crystal structure of N-acetylneuraminate lyase from E. coli mutant L142R in complex with b-hydroxypyruvate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mimicking Natural Evolution in Vitro: An N-Acetylneuraminate Lyase Mutant with an Increased Dihydrodipicolinate Synthase Activity

Joerger, A.C.Mayer, S.Fersht, A.R.

(2003) Proc.Natl.Acad.Sci.USA 100: 5694

  • DOI: 10.1073/pnas.0531477100

  • PubMed Abstract: 
  • N-acetylneuraminate lyase (NAL) and dihydrodipicolinate synthase (DHDPS) belong to the NAL subfamily of (betaalpha)(8)-barrels. They share a common catalytic step but catalyze reactions in different biological pathways. By rational design, we have in ...

    N-acetylneuraminate lyase (NAL) and dihydrodipicolinate synthase (DHDPS) belong to the NAL subfamily of (betaalpha)(8)-barrels. They share a common catalytic step but catalyze reactions in different biological pathways. By rational design, we have introduced various mutations into the NAL scaffold from Escherichia coli to switch the activity toward DHDPS. These mutants were tested with respect to their catalytic properties in vivo and in vitro as well as their stability. One point mutation (L142R) was sufficient to create an enzyme that could complement a bacterial auxotroph lacking the gene for DHDPS as efficiently as DHDPS itself. In vitro, this mutant had an increased DHDPS activity of up to 19-fold as defined by the specificity constant k(cat)K(M) for the new substrate l-aspartate-beta-semialdehyde when compared with the residual activity of NAL wild-type, mainly because of an increased turnover rate. At the same time, mutant L142R maintained much of its original NAL activity. We have solved the crystal structure of mutant L142R at 1.8 A resolution in complex with the inhibitor beta-hydroxypyruvate. This structure reveals that the conformations of neighboring active site residues are left virtually unchanged by the mutation. The high flexibility of R142 may favor its role in assisting in catalysis. Perhaps, nature has exploited the catalytic promiscuity of many enzymes to evolve novel enzymes or biological pathways during the course of evolution.


    Related Citations: 
    • The Three-Dimensional Structure of N-Acetylneuraminate Lyase from Escherichia Coli
      Izard, T.,Lawrence, M.C.,Malby, R.,Lilley, G.G.,Colman, P.M.
      (1994) Structure 2: 361
    • Structure and Mechanism of a Sub-Family of Enzymes Related to N-Acetylneuraminate Lyase
      Lawrence, M.C.,Barbosa, J.A.,Smith, B.J.,Hall, N.E.,Pilling, P.A.,Ooi, H.C.,Marcuccio, S.M.
      (1997) J.Mol.Biol. 266: 381


    Organizational Affiliation

    Cambridge University Chemical Laboratory and Cambridge Centre for Protein Engineering, Medical Research Council Centre, Hills Road, Cambridge CB2 2QH, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-ACETYLNEURAMINATE LYASE SUBUNIT
A, B, C, D
297Escherichia coli (strain K12)Mutation(s): 1 
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: 1.8 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 83.740α = 90.00
b = 95.990β = 115.16
c = 89.650γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-05-09
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance