4P3M

Crystal structure of serine hydroxymethyltransferase from Psychromonas ingrahamii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Conformational transitions driven by pyridoxal-5'-phosphate uptake in the psychrophilic serine hydroxymethyltransferase from Psychromonas ingrahamii.

Angelaccio, S.Dworkowski, F.Di Bello, A.Milano, T.Capitani, G.Pascarella, S.

(2014) Proteins 82: 2831-2841

  • DOI: 10.1002/prot.24646

  • PubMed Abstract: 
  • Serine hydroxymethyltransferase (SHMT) is a pyridoxal-5'-phosphate (PLP)-dependent enzyme belonging to the fold type I superfamily, which catalyzes in vivo the reversible conversion of l-serine and tetrahydropteroylglutamate (H₄PteGlu) to glycine and ...

    Serine hydroxymethyltransferase (SHMT) is a pyridoxal-5'-phosphate (PLP)-dependent enzyme belonging to the fold type I superfamily, which catalyzes in vivo the reversible conversion of l-serine and tetrahydropteroylglutamate (H₄PteGlu) to glycine and 5,10-methylenetetrahydropteroylglutamate (5,10-CH₂-H₄PteGlu). The SHMT from the psychrophilic bacterium Psychromonas ingrahamii (piSHMT) had been recently purified and characterized. This enzyme was shown to display catalytic and stability properties typical of psychrophilic enzymes, namely high catalytic activity at low temperature and thermolability. To gain deeper insights into the structure-function relationship of piSHMT, the three-dimensional structure of its apo form was determined by X-ray crystallography. Homology modeling techniques were applied to build a model of the piSHMT holo form. Comparison of the two forms unraveled the conformation modifications that take place when the apo enzyme binds its cofactor. Our results show that the apo form is in an "open" conformation and possesses four (or five, in chain A) disordered loops whose electron density is not visible by X-ray crystallography. These loops contain residues that interact with the PLP cofactor and three of them are localized in the major domain that, along with the small domain, constitutes the single subunit of the SHMT homodimer. Cofactor binding triggers a rearrangement of the small domain that moves toward the large domain and screens the PLP binding site at the solvent side. Comparison to the mesophilic apo SHMT from Salmonella typhimurium suggests that the backbone conformational changes are wider in psychrophilic SHMT.


    Organizational Affiliation

    Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Università La Sapienza, 00185, Roma, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine hydroxymethyltransferase
A, B
429Psychromonas ingrahamii (strain 37)Mutation(s): 0 
Gene Names: glyA
EC: 2.1.2.1
Find proteins for A1SUU0 (Psychromonas ingrahamii (strain 37))
Go to UniProtKB:  A1SUU0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.169 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 146.820α = 90.00
b = 64.860β = 125.49
c = 116.940γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2014-08-20
    Type: Database references
  • Version 1.2: 2014-10-08
    Type: Database references