1LW5

X-ray structure of L-Threonine Aldolase (low-specificity) in complex with glycine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

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This is version 1.3 of the entry. See complete history


Literature

X-ray Structures of Threonine Aldolase Complexes: Structural Basis of Substrate Recognition

Kielkopf, C.L.Burley, S.K.

(2002) Biochemistry 41: 11711-11720

  • DOI: 10.1021/bi020393+
  • Primary Citation of Related Structures:  
    1M6S, 1LW5, 1LW4

  • PubMed Abstract: 
  • L-Threonine acetaldehyde-lyase (threonine aldolase, TA) is a pyridoxal-5'-phosphate-dependent (PLP) enzyme that catalyzes conversion of L-threonine or L-allo-threonine to glycine and acetaldehyde in a secondary glycine biosynthetic pathway. X-ray structures of Thermatoga maritima TA have been determined as the apo-enzyme at 1 ...

    L-Threonine acetaldehyde-lyase (threonine aldolase, TA) is a pyridoxal-5'-phosphate-dependent (PLP) enzyme that catalyzes conversion of L-threonine or L-allo-threonine to glycine and acetaldehyde in a secondary glycine biosynthetic pathway. X-ray structures of Thermatoga maritima TA have been determined as the apo-enzyme at 1.8 A resolution and bound to substrate L-allo-threonine and product glycine at 1.9 and 2.0 A resolution, respectively. Despite low pairwise sequence identities, TA is a member of aspartate aminotransferase (AATase) fold family of PLP enzymes. The enzyme forms a 222 homotetramer with the PLP cofactor bound via a Schiff-base linkage to Lys199 within a domain interface. The structure reveals bound calcium and chloride ions that appear to contribute to catalysis and oligomerization, respectively. Although L-threonine and L-allo-threonine are substrates for T. maritima TA, enzymatic assays revealed a strong preference for L-allo-threonine. Structures of the external aldimines with substrate/product reveal a pair of histidines that may provide flexibility in substrate recognition. Variation in the threonine binding pocket may explain preferences for L-allo-threonine versus L-threonine among TA family members.


    Organizational Affiliation

    Laboratories of Molecular Biophysics and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-allo-threonine aldolaseA, B, C, D347Thermotoga maritimaMutation(s): 0 
EC: 4.1.2.5
UniProt
Find proteins for Q9X266 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X266 
Go to UniProtKB:  Q9X266
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLG (Subject of Investigation/LOI)
Query on PLG

Download Ideal Coordinates CCD File 
L [auth B], O [auth C], T [auth D]N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]
C10 H15 N2 O7 P
FEVQWBMNLWUBTF-UHFFFAOYSA-N
 Ligand Interaction
PLP (Subject of Investigation/LOI)
Query on PLP

Download Ideal Coordinates CCD File 
M [auth B]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], H [auth B], I [auth B], N [auth C], P [auth D]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A], J [auth B], K [auth B], Q [auth D], R [auth D], S [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A, B, C, DL-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
MSE
Query on MSE
A, B, C, DL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.02α = 90
b = 100.71β = 90
c = 150.2γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-11
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2021-02-03
    Changes: Database references, Derived calculations, Structure summary