5Z0Y

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


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 

wwPDB Validation   3D Report Full Report



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

  • 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 ...

    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.


    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: chenzhongzhou@cau.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine hydroxymethyltransferaseA470Komagataella phaffii CBS 7435Mutation(s): 0 
Gene Names: SHM2PP7435_Chr4-0570
EC: 2.1.2.1
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
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 = 105.315α = 90
b = 114.743β = 90
c = 84.157γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

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

Funding OrganizationLocationGrant Number
National Key Research and Development Program of ChinaChina2016YFC1200400

Revision History 

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