4LNL

Structure of Escherichia coli Threonine Aldolase in Complex with Allo-Thr

  • Classification: LYASE
  • Expression System: Escherichia coli
  • Mutation(s): 

  • Deposited: 2013-07-11 Released: 2013-11-06 
  • Deposition Author(s): Safo, M.K.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

On the catalytic mechanism and stereospecificity of Escherichia coli l-threonine aldolase.

di Salvo, M.L.Remesh, S.G.Vivoli, M.Ghatge, M.S.Paiardini, A.D'Aguanno, S.Safo, M.K.Contestabile, R.

(2014) Febs J. 281: 129-145

  • DOI: 10.1111/febs.12581
  • Primary Citation of Related Structures:  4LNJ, 4LNM

  • PubMed Abstract: 
  • L-threonine aldolases (L-TAs) represent a family of homologous pyridoxal 5'-phosphate-dependent enzymes found in bacteria and fungi, and catalyse the reversible cleavage of several L-3-hydroxy-α-amino acids. L-TAs have great biotechnological potentia ...

    L-threonine aldolases (L-TAs) represent a family of homologous pyridoxal 5'-phosphate-dependent enzymes found in bacteria and fungi, and catalyse the reversible cleavage of several L-3-hydroxy-α-amino acids. L-TAs have great biotechnological potential, as they catalyse the formation of carbon-carbon bonds, and therefore may be exploited for the bioorganic synthesis of L-3-hydroxyamino acids that are biologically active or constitute building blocks for pharmaceutical molecules. Many L-TAs, showing different stereospecificity towards the Cβ configuration, have been isolated. Because of their potential to carry out diastereoselective syntheses, L-TAs have been subjected to structural, functional and mechanistic studies. Nevertheless, their catalytic mechanism and the structural bases of their stereospecificity have not been elucidated. In this study, we have determined the crystal structure of low-specificity L-TA from Escherichia coli at 2.2-Å resolution, in the unliganded form and cocrystallized with L-serine and L-threonine. Furthermore, several active site mutants have been functionally characterized in order to elucidate the reaction mechanism and the molecular bases of stereospecificity. No active site catalytic residue was revealed, and a structural water molecule was assumed to act as the catalytic base in the retro-aldol cleavage reaction. Interestingly, the very large active site opening of E. coli L-TA suggests that much larger molecules than L-threonine isomers may be easily accommodated, and L-TAs may actually have diverse physiological functions in different organisms. Substrate recognition and reaction specificity seem to be guided by the overall microenvironment that surrounds the substrate at the enzyme active site, rather than by one ore more specific residues.


    Organizational Affiliation

    Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Low-specificity L-threonine aldolase
A, B
333N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

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Download CCD File 
A, B
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
2BO
Query on 2BO

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Download CCD File 
A
N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-threonine
C12 H19 N2 O8 P
IZWQBQLGLAKRMN-XCBNKYQSSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PLG
Query on PLG

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B
N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]
N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE
C10 H15 N2 O7 P
FEVQWBMNLWUBTF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
2BK
Query on 2BK

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Download CCD File 
A
N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-allothreonine
C12 H19 N2 O8 P
IZWQBQLGLAKRMN-XVKPBYJWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.182 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 76.400α = 90.00
b = 100.890β = 90.00
c = 176.000γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata scaling
CrystalCleardata collection
CNSrefinement
d*TREKdata reduction
caspRphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-07-11 
  • Released Date: 2013-11-06 
  • Deposition Author(s): Safo, M.K.

Revision History 

  • Version 1.0: 2013-11-06
    Type: Initial release
  • Version 1.1: 2014-01-22
    Type: Database references