2VMY

Crystal structure of F351GbsSHMT in complex with Gly and FTHF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SERINE HYDROXYMETHYLTRANSFERASE
A, B
405Geobacillus stearothermophilusMutation(s): 1 
EC: 2.1.2.1
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FFO
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
VVIAGPKUTFNRDU-STQMWFEESA-N
PLP
Query on PLP

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
MRD
Query on MRD

Download Ideal Coordinates CCD File 
I [auth B](4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
GLY
Query on GLY

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing

Structure Validation

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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