4WXG

Crystal structure of L-Serine Hydroxymethyltransferase in complex with a mixture of L-allo-Threonine and Glycine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Engineered L-Serine Hydroxymethyltransferase from Streptococcus thermophilus for the Synthesis of alpha , alpha-Dialkyl-alpha-Amino Acids.

Hernandez, K.Zelen, I.Petrillo, G.Uson, I.Wandtke, C.M.Bujons, J.Joglar, J.Parella, T.Clapes, P.

(2015) Angew.Chem.Int.Ed.Engl. 54: 3013-3017

  • DOI: 10.1002/anie.201411484
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • α,α-Disubstituted α-amino acids are central to biotechnological and biomedical chemical processes for their own sake and as substructures of biologically active molecules for diverse biomedical applications. Structurally, these compounds contain a qu ...

    α,α-Disubstituted α-amino acids are central to biotechnological and biomedical chemical processes for their own sake and as substructures of biologically active molecules for diverse biomedical applications. Structurally, these compounds contain a quaternary stereocenter, which is particularly challenging for stereoselective synthesis. The pyridoxal-5'-phosphate (PLP)-dependent L-serine hydroxymethyltransferase from Streptococcus thermophilus (SHMT(Sth); EC 2.1.2.1) was engineered to achieve the stereoselective synthesis of a broad structural variety of α,α-dialkyl-α-amino acids. This was accomplished by the formation of quaternary stereocenters through aldol addition of the amino acids D-Ala and D-Ser to a wide acceptor scope catalyzed by the minimalist SHMT(Sth) Y55T variant overcoming the limitation of the native enzyme for Gly. The SHMT(Sth) Y55T variant tolerates aromatic and aliphatic aldehydes as well as hydroxy- and nitrogen-containing aldehydes as acceptors.


    Organizational Affiliation

    Dept Química Biológica y Modelización Molecular, Instituto de Química Avanzada de Cataluña, IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona (Spain).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine hydroxymethyltransferase
A, C
428Streptococcus thermophilus (strain CNRZ 1066)Mutation(s): 0 
Gene Names: glyA
EC: 2.1.2.1
Find proteins for Q5M0B4 (Streptococcus thermophilus (strain CNRZ 1066))
Go to UniProtKB:  Q5M0B4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2BO
Query on 2BO

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

Download SDF File 
Download CCD File 
A, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 115.430α = 90.00
b = 115.430β = 90.00
c = 191.480γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
MOLREPphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministerio de Ciencia e InnovacionSpainBIO2006-14139
Spanish Ministry of Economy and CompetitivenessSpainBFU2012-35367

Revision History 

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 1.1: 2015-03-04
    Type: Database references
  • Version 2.0: 2017-09-13
    Type: Advisory, Atomic model, Author supporting evidence, Derived calculations