5Z0Y

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

PDB DOI: https://doi.org/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

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

This is version 1.1 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/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.

Organizational Affiliation

Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.

Macromolecule Content

Total Structure Weight: 52.24 kDa
Atom Count: 2,860
Modelled Residue Count: 372
Deposited Residue Count: 470
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F2QZA4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]