1EQB

X-RAY CRYSTAL STRUCTURE AT 2.7 ANGSTROMS RESOLUTION OF TERNARY COMPLEX BETWEEN THE Y65F MUTANT OF E-COLI SERINE HYDROXYMETHYLTRANSFERASE, GLYCINE AND 5-FORMYL TETRAHYDROFOLATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Role of tyrosine 65 in the mechanism of serine hydroxymethyltransferase.

Contestabile, R.Angelaccio, S.Bossa, F.Wright, H.T.Scarsdale, N.Kazanina, G.Schirch, V.

(2000) Biochemistry 39: 7492-7500


  • PubMed Abstract: 
  • Crystal structures of human and rabbit cytosolic serine hydroxymethyltransferase have shown that Tyr65 is likely to be a key residue in the mechanism of the enzyme. In the ternary complex of Escherichia coli serine hydroxymethyltransferase with glyci ...

    Crystal structures of human and rabbit cytosolic serine hydroxymethyltransferase have shown that Tyr65 is likely to be a key residue in the mechanism of the enzyme. In the ternary complex of Escherichia coli serine hydroxymethyltransferase with glycine and 5-formyltetrahydrofolate, the hydroxyl of Tyr65 is one of four enzyme side chains within hydrogen-bonding distance of the carboxylate group of the substrate glycine. To probe the role of Tyr65 it was changed by site-directed mutagenesis to Phe65. The three-dimensional structure of the Y65F site mutant was determined and shown to be isomorphous with the wild-type enzyme except for the missing Tyr hydroxyl group. The kinetic properties of this mutant enzyme in catalyzing reactions with serine, glycine, allothreonine, D- and L-alanine, and 5,10-methenyltetrahydrofolate substrates were determined. The properties of the enzyme with D- and L-alanine, glycine in the absence of tetrahydrofolate, and 5, 10-methenyltetrahydrofolate were not significantly changed. However, catalytic activity was greatly decreased for serine and allothreonine cleavage and for the solvent alpha-proton exchange of glycine in the presence of tetrahydrofolate. The decreased catalytic activity for these reactions could be explained by a greater than 2 orders of magnitude increase in affinity of Y65F mutant serine hydroxymethyltransferase for these amino acids bound as the external aldimine. These data are consistent with a role for the Tyr65 hydroxyl group in the conversion of a closed active site to an open structure.


    Related Citations: 
    • Crystal Structure at 2.4 Angstrom Resolution of E. Coli Serine Hydroxymethyltransferase in Complex with Glycine Substrate and 5-Formyl Tetrahydrofolate
      Scarsdale, J.N.,Radaev, S.,Kazanina, G.,Schirch, V.,Wright, H.T.
      (2000) J.Mol.Biol. 296: 155


    Organizational Affiliation

    Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Centro di Biologia Molecolare del Consiglio Nazionale delle Ricerche, Università La Sapienza, Roma, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SERINE HYDROXYMETHYLTRANSFERASE
A, B, C, D
417Escherichia coli (strain K12)Gene Names: glyA
EC: 2.1.2.1
Find proteins for P0A825 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A825
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLY
Query on GLY

Download SDF File 
Download CCD File 
A, B, C, D
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
FFO
Query on FFO

Download SDF File 
Download CCD File 
A, B, C, D
N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid
[6S]-5-FORMYL-TETRAHYDROFOLATE; 6S-FOLINIC ACID
C20 H23 N7 O7
VVIAGPKUTFNRDU-STQMWFEESA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, B, C, D
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 77.740α = 90.00
b = 172.480β = 104.28
c = 95.410γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-04-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2014-05-07
    Type: Other