Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 93.84 kDa 
• Atom Count: 6481 
• Modelled Residue Count: 765 
• Deposited Residue Count: 858 
• Unique protein chains: 1

4P3M

Crystal structure of serine hydroxymethyltransferase from Psychromonas ingrahamii

• PDB DOI: 10.2210/pdb4P3M/pdb

• Classification: TRANSFERASE
• Organism(s): Psychromonas ingrahamii 37
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-03-09 Released: 2014-07-30 
• Deposition Author(s): Dworkowski, F., Angelaccio, S., Pascarella, S., Capitani, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.212 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 

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

• PubMed: 25044250 
• DOI: 10.1002/prot.24646
• Primary Citation of Related Structures:  
  4P3M


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase	A, B	429	Psychromonas ingrahamii 37	Mutation(s): 0  Gene Names: glyA, Ping_1438 EC: 2.1.2.1
UniProt
Find proteins for A1SUU0 (Psychromonas ingrahamii (strain 37)) Explore A1SUU0  Go to UniProtKB:  A1SUU0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], N [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	J [auth A], K [auth A], L [auth A], M [auth A], O [auth B], P [auth B], Q [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	G [auth A], H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.212 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.82	α = 90
b = 64.86	β = 125.49
c = 116.94	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-03-09 
• Released Date: 2014-07-30 
Deposition Author(s): Dworkowski, F., Angelaccio, S., Pascarella, S., Capitani, G.

Revision History  

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