4PVF

Crystal structure of Homo sapiens holo serine hydroxymethyltransferase 2 (mitochondrial) (SHMT2), isoform 3, transcript variant 5, 483 aa, at 2.6 ang. resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

How pyridoxal 5'-phosphate differentially regulates human cytosolic and mitochondrial serine hydroxymethyltransferase oligomeric state.

Giardina, G.Brunotti, P.Fiascarelli, A.Cicalini, A.Costa, M.G.Buckle, A.M.di Salvo, M.L.Giorgi, A.Marani, M.Paone, A.Rinaldo, S.Paiardini, A.Contestabile, R.Cutruzzola, F.

(2015) Febs J. 282: 1225-1241

  • DOI: 10.1111/febs.13211

  • PubMed Abstract: 
  • Adaptive metabolic reprogramming gives cancer cells a proliferative advantage. Tumour cells extensively use glycolysis to sustain anabolism and produce serine, which not only refuels the one-carbon units necessary for the synthesis of nucleotide prec ...

    Adaptive metabolic reprogramming gives cancer cells a proliferative advantage. Tumour cells extensively use glycolysis to sustain anabolism and produce serine, which not only refuels the one-carbon units necessary for the synthesis of nucleotide precursors and for DNA methylation, but also affects the cellular redox homeostasis. Given its central role in serine metabolism, serine hydroxymethyltransferase (SHMT), a pyridoxal 5'-phosphate (PLP)-dependent enzyme, is an attractive target for tumour chemotherapy. In humans, the cytosolic isoform (SHMT1) and the mitochondrial isoform (SHMT2) have distinct cellular roles, but high sequence identity and comparable catalytic properties, which may complicate development of successful therapeutic strategies. Here, we investigated how binding of the cofactor PLP controls the oligomeric state of the human isoforms. The fact that eukaryotic SHMTs are tetrameric proteins while bacterial SHMTs function as dimers may suggest that the quaternary assembly in eukaryotes provides an advantage to fine-tune SHMT function and differentially regulate intertwined metabolic fluxes, and may provide a tool to address the specificity problem. We determined the crystal structure of SHMT2, and compared it to the apo-enzyme structure, showing that PLP binding triggers a disorder-to-order transition accompanied by a large rigid-body movement of the two cofactor-binding domains. Moreover, we demonstrated that SHMT1 exists in solution as a tetramer, both in the absence and presence of PLP, while SHMT2 undergoes a dimer-to-tetramer transition upon PLP binding. These findings indicate an unexpected structural difference between the two human SHMT isoforms, which opens new perspectives for understanding their differing behaviours, roles or regulation mechanisms in response to PLP availability in vivo.


    Organizational Affiliation

    Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza UniversitĂ  di Roma, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine hydroxymethyltransferase, mitochondrial
A, B
483Homo sapiensMutation(s): 0 
Gene Names: SHMT2
EC: 2.1.2.1
Find proteins for P34897 (Homo sapiens)
Go to Gene View: SHMT2
Go to UniProtKB:  P34897
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A, B
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.206 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 160.462α = 90.00
b = 160.462β = 90.00
c = 211.461γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
XDSdata reduction
XDSdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2015-02-25
    Type: Database references
  • Version 1.2: 2015-04-22
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Refinement description