Joint X-ray/neutron structure of Thermus thermophilus serine hydroxymethyltransferase (TthSHMT) in internal aldimine state with L-Ser bound in a pre-Michalis complex

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.166 

  • Resolution: 2.30 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.204 

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Revealing protonation states and tracking substrate in serine hydroxymethyltransferase with room-temperature X-ray and neutron crystallography.

Drago, V.N.Campos, C.Hooper, M.Collins, A.Gerlits, O.Weiss, K.L.Blakeley, M.P.Phillips, R.S.Kovalevsky, A.

(2023) Commun Chem 6: 162-162

  • DOI: https://doi.org/10.1038/s42004-023-00964-9
  • Primary Citation of Related Structures:  
    8SSJ, 8SSY, 8SUI, 8SUJ

  • PubMed Abstract: 

    Pyridoxal 5'-phosphate (PLP)-dependent enzymes utilize a vitamin B 6 -derived cofactor to perform a myriad of chemical transformations on amino acids and other small molecules. Some PLP-dependent enzymes, such as serine hydroxymethyltransferase (SHMT), are promising drug targets for the design of small-molecule antimicrobials and anticancer therapeutics, while others have been used to synthesize pharmaceutical building blocks. Understanding PLP-dependent catalysis and the reaction specificity is crucial to advance structure-assisted drug design and enzyme engineering. Here we report the direct determination of the protonation states in the active site of Thermus thermophilus SHMT (TthSHMT) in the internal aldimine state using room-temperature joint X-ray/neutron crystallography. Conserved active site architecture of the model enzyme TthSHMT and of human mitochondrial SHMT (hSHMT2) were compared by obtaining a room-temperature X-ray structure of hSHMT2, suggesting identical protonation states in the human enzyme. The amino acid substrate serine pathway through the TthSHMT active site cavity was tracked, revealing the peripheral and cationic binding sites that correspond to the pre-Michaelis and pseudo-Michaelis complexes, respectively. At the peripheral binding site, the substrate is bound in the zwitterionic form. By analyzing the observed protonation states, Glu53, but not His residues, is proposed as the general base catalyst, orchestrating the retro-aldol transformation of L-serine into glycine.

  • Organizational Affiliation

    Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine hydroxymethyltransferase
A, B
405Thermus thermophilus HB8Mutation(s): 0 
Gene Names: glyATTHA1524
Find proteins for Q5SI56 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SI56 
Go to UniProtKB:  Q5SI56
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SI56
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on LLP
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.166 
  • Space Group: P 1 21 1
  • Resolution: 2.30 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.807α = 90
b = 83.334β = 91.68
c = 95.568γ = 90
Software Package:
Software NamePurpose
CrysalisProdata reduction
CrysalisProdata scaling
Mantiddata reduction
SCALAdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM137008-01A1

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Data collection