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 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content

• Total Structure Weight: 52.24 kDa 
• Atom Count: 2860 
• Modelled Residue Count: 372 
• Deposited Residue Count: 470 
• Unique protein chains: 1

5Z0Y

Crystallization and structure determination of cytoplasm serine hydroxymethyltransferase (SHMT) from Pichia pastoris

• PDB DOI: 10.2210/pdb5Z0Y/pdb

• Classification: TRANSFERASE
• Organism(s): Komagataella phaffii CBS 7435
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2017-12-22 Released: 2018-03-14 
• Deposition Author(s): Chen, Z., Zhang, M.
• Funding Organization(s): National Key Research and Development Program of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.260 
• R-Value Work: 0.227 
• R-Value Observed: 0.228 

Literature

Structure and function of cytoplasmic serine hydroxymethyltransferase from Pichia pastoris

Zhang, M., Wu, W., Chen, Z.

(2018) Biochem Biophys Res Commun 496: 753-757

• PubMed: 29339156 
• DOI: 10.1016/j.bbrc.2018.01.084
• Primary Citation of Related Structures:  
  5Z0Y


• PubMed Abstract: 
  

Serine hydroxymethyltransferase (SHMT) catalyzes the interconversion of serine and glycine, which is crucial for one carbon metabolism. Here, we report the first crystal structure of cytoplasmic SHMT from Pichia pastoris (pcSHMT) diffracted to 2.5 Å resolution in space group C222 ₁ . PcSHMT was a contaminant with our target protein expressed in Pichia pastoris and confirmed by mass spectrometry. The overall structure of pcSHMT is similar to Human mitochondrial SHMT and different to E. coli SHMT. Interestingly, the oligomerization of pcSHMT expressed in eukaryotic or prokaryotic system differs significantly and is regulated by pyridoxal-5'-phosphate. Our results revealed a close evolutionary relationship between Pichia pastoris and Human mitochondria.

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Organizational Affiliation: 

Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase	A	470	Komagataella phaffii CBS 7435	Mutation(s): 0  Gene Names: SHM2, PP7435_Chr4-0570 EC: 2.1.2.1
UniProt
Find proteins for F2QZA4 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)) Explore F2QZA4  Go to UniProtKB:  F2QZA4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.260 
• R-Value Work: 0.227 
• R-Value Observed: 0.228 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.315	α = 90
b = 114.743	β = 90
c = 84.157	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
BALBES	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-12-22 
• Released Date: 2018-03-14 
Deposition Author(s): Chen, Z., Zhang, M.

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Funding Organization	Location	Grant Number
National Key Research and Development Program of China	China	2016YFC1200400

Revision History  

• Version 1.0: 2018-03-14
  Type: Initial release