Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 187.93 kDa 
• Atom Count: 13047 
• Modelled Residue Count: 1620 
• Deposited Residue Count: 1712 
• Unique protein chains: 1

4WXB

Crystal Structure of Serine Hydroxymethyltransferase from Streptococcus thermophilus

• PDB DOI: 10.2210/pdb4WXB/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus thermophilus CNRZ1066
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-11-13 Released: 2015-02-04 
• Deposition Author(s): Hernandez, K., Zelen, I., Petrillo, G., Uson, I., Wandtke, C., Bujons, J., Joglar, J., Parella, T., Clapes, P.
• Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities, Spanish Ministry of Economy and Competitiveness

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.221 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

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

• PubMed: 25611820 
• DOI: 10.1002/anie.201411484
• Primary Citation of Related Structures:  
  4WXB, 4WXF, 4WXG


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase	A, B, C, D	428	Streptococcus thermophilus CNRZ1066	Mutation(s): 0  Gene Names: glyA, str0755 EC: 2.1.2.1
UniProt
Find proteins for Q5M0B4 (Streptococcus thermophilus (strain CNRZ 1066)) Explore Q5M0B4  Go to UniProtKB:  Q5M0B4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT (Subject of Investigation/LOI)	E [auth A], H [auth B], L [auth C], P [auth D]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
CAC (Subject of Investigation/LOI)	F [auth A], I [auth B], M [auth C], Q [auth D]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
GOL (Subject of Investigation/LOI)	G [auth A], K [auth B], O [auth C], S [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)	J [auth B], N [auth C], R [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.221 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 202.104	α = 90
b = 113.431	β = 93.85
c = 133.388	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2014-11-13 
• Released Date: 2015-02-04 
Deposition Author(s): Hernandez, K., Zelen, I., Petrillo, G., Uson, I., Wandtke, C., Bujons, J., Joglar, J., Parella, T., Clapes, P.

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Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	BIO2006-14139
Spanish Ministry of Economy and Competitiveness	Spain	BFU2012-35367

Revision History  

• Version 1.0: 2015-02-04
  Type: Initial release
  
• Version 1.1: 2015-03-04
  Changes: Database references
• Version 2.0: 2017-09-13
  Changes: Atomic model, Author supporting evidence, Derived calculations
• Version 3.0: 2019-10-23
  Type: Coordinate replacement
  Reason: Sequence discrepancy
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary