Crystal Structure of the Complex between Rabbit Cytosolic Serine Hydroxymethyltransferase and TriGlu-5-formyl-tetrahydrofolate

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 

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Location of the Pteroylpolyglutamate Binding Site on Rabbit Cytosolic Serine Hydroxymethyltransferase

Fu, T.F.Scarsdale, J.N.Kazanina, G.Schirch, V.Wright, H.T.

(2003) J Biol Chem 278: 2645-2653

  • DOI: https://doi.org/10.1074/jbc.M210649200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Serine hydroxymethyltransferase (SHMT; EC catalyzes the reversible interconversion of serine and glycine with transfer of the serine side chain one-carbon group to tetrahydropteroylglutamate (H(4)PteGlu), and also the conversion of 5,10-methenyl-H(4)PteGlu to 5-formyl-H(4)PteGlu. In the cell, H(4)PteGlu carries a poly-gamma-glutamyl tail of at least 3 glutamyl residues that is required for physiological activity. This study combines solution binding and mutagenesis studies with crystallographic structure determination to identify the extended binding site for tetrahydropteroylpolyglutamate on rabbit cytosolic SHMT. Equilibrium binding and kinetic measurements of H(4)PteGlu(3) and H(4)PteGlu(5) with wild-type and Lys --> Gln or Glu site mutant homotetrameric rabbit cytosolic SHMTs identified lysine residues that contribute to the binding of the polyglutamate tail. The crystal structure of the enzyme in complex with 5-formyl-H(4)PteGlu(3) confirms the solution data and indicates that the conformation of the pteridine ring and its interactions with the enzyme differ slightly from those observed in complexes of the monoglutamate cofactor. The polyglutamate chain, which does not contribute to catalysis, exists in multiple conformations in each of the two occupied binding sites and appears to be bound by the electrostatic field created by the cationic residues, with only limited interactions with specific individual residues.

  • Organizational Affiliation

    Department of Biochemistry and the Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond 23219-1570, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine Hydroxymethyltransferase
A, B, C, D
483Oryctolagus cuniculusMutation(s): 0 
Find proteins for P07511 (Oryctolagus cuniculus)
Explore P07511 
Go to UniProtKB:  P07511
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07511
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on TGF

Download Ideal Coordinates CCD File 
H [auth B],
O [auth D]
C30 H37 N9 O13
Query on PLP

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E [auth A],
G [auth B],
L [auth C],
N [auth D]
C8 H10 N O6 P
Query on GOL

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I [auth B],
J [auth B],
M [auth C],
P [auth D]
C3 H8 O3
Query on GLY

Download Ideal Coordinates CCD File 
F [auth A],
K [auth C]
C2 H5 N O2
Binding Affinity Annotations 
IDSourceBinding Affinity
TGF BindingDB:  1LS3 ΔH: 24.66 (kJ/mol) from 1 assay(s)
ΔG: -4.05e+1 (kJ/mol) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.084α = 90
b = 114.084β = 90
c = 156.719γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-04
    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: 2013-08-21
    Changes: Non-polymer description
  • Version 1.4: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary