Crystal structure of F351GbsSHMT in complex with Gly and FTHF

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Structural and Functional Studies of Bacillus Stearothermophilus Serine Hydroxymethyltransferase: The Role of Asn(341), Tyr(60) and Phe(351) in Tetrahydrofolate Binding.

Pai, V.R.Rajaram, V.Bisht, S.Bhavani, B.S.Rao, N.A.Murthy, M.R.N.Savithri, H.S.

(2009) Biochem J 418: 635

  • DOI: https://doi.org/10.1042/BJ20081739
  • Primary Citation of Related Structures:  
    2VMN, 2VMO, 2VMP, 2VMQ, 2VMR, 2VMS, 2VMT, 2VMU, 2VMV, 2VMW, 2VMX, 2VMY, 2VMZ

  • PubMed Abstract: 

    SHMT (serine hydoxymethyltransferase), a type I pyridoxal 5'-phosphate-dependent enzyme, catalyses the conversion of L-serine and THF (tetrahydrofolate) into glycine and 5,10-methylene THF. SHMT also catalyses several THF-independent side reactions such as cleavage of beta-hydroxy amino acids, transamination, racemization and decarboxylation. In the present study, the residues Asn(341), Tyr(60) and Phe(351), which are likely to influence THF binding, were mutated to alanine, alanine and glycine respectively, to elucidate the role of these residues in THF-dependent and -independent reactions catalysed by SHMT. The N341A and Y60A bsSHMT (Bacillus stearothermophilus SHMT) mutants were inactive for the THF-dependent activity, while the mutations had no effect on THF-independent activity. However, mutation of Phe(351) to glycine did not have any effect on either of the activities. The crystal structures of the glycine binary complexes of the mutants showed that N341A bsSHMT forms an external aldimine as in bsSHMT, whereas Y60A and F351G bsSHMTs exist as a mixture of internal/external aldimine and gem-diamine forms. Crystal structures of all of the three mutants obtained in the presence of L-allo-threonine were similar to the respective glycine binary complexes. The structure of the ternary complex of F351G bsSHMT with glycine and FTHF (5-formyl THF) showed that the monoglutamate side chain of FTHF is ordered in both the subunits of the asymmetric unit, unlike in the wild-type bsSHMT. The present studies demonstrate that the residues Asn(341) and Tyr(60) are pivotal for the binding of THF/FTHF, whereas Phe(351) is responsible for the asymmetric binding of FTHF in the two subunits of the dimer.

  • Organizational Affiliation

    Department of Biochemistry, Indian Institute of Science, Bangalore, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
405Geobacillus stearothermophilusMutation(s): 1 
Find proteins for Q7SIB6 (Geobacillus stearothermophilus)
Explore Q7SIB6 
Go to UniProtKB:  Q7SIB6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SIB6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FFO

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid
C20 H23 N7 O7
Query on PLP

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
C8 H10 N O6 P
Query on MRD

Download Ideal Coordinates CCD File 
C6 H14 O2
Query on GLY

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
C2 H5 N O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.382α = 90
b = 103.483β = 90.33
c = 61.959γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-16
    Type: Initial release
  • Version 1.1: 2011-09-14
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description