5AX7 | pdb_00005ax7

yeast pyruvyltransferase Pvg1p

• PDB DOI: https://doi.org/10.2210/pdb5AX7/pdb

• Classification: TRANSFERASE
• Organism(s): Schizosaccharomyces pombe 972h-
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-07-16 Released: 2016-06-08 
• Deposition Author(s): Kanekiyo, M., Yoritsune, K., Yoshinaga, S., Higuchi, Y., Takegawa, K., Kakuta, Y.
• Funding Organization(s): a Grant-in-Aid for Scientific Research from the Ministry of Education, Science, and Culture of Japan

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 
  0.183 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

A rationally engineered yeast pyruvyltransferase Pvg1p introduces sialylation-like properties in neo-human-type complex oligosaccharide

Higuchi, Y., Yoshinaga, S., Yoritsune, K., Tateno, H., Hirabayashi, J., Nakakita, S., Kanekiyo, M., Kakuta, Y., Takegawa, K.

(2016) Sci Rep 6: 26349-26349

• PubMed: 27194449 
• DOI: https://doi.org/10.1038/srep26349
• Primary Citation Related Structures: 
  5AX7


• PubMed Abstract: 
  

  Pyruvylation onto the terminus of oligosaccharide, widely seen from prokaryote to eukaryote, confers negative charges on the cell surface and seems to be functionally similar to sialylation, which is found at the end of human-type complex oligosaccharide. However, detailed molecular mechanisms underlying pyruvylation have not been clarified well. Here, we first determined the crystal structure of fission yeast pyruvyltransferase Pvg1p at a resolution of 2.46 Å. Subsequently, by combining molecular modeling with mutational analysis of active site residues, we obtained a Pvg1p mutant (Pvg1p(H168C)) that efficiently transferred pyruvyl moiety onto a human-type complex glycopeptide. The resultant pyruvylated human-type complex glycopeptide recognized similar lectins on lectin arrays as the α2,6-sialyl glycopeptides. This newly-generated pyruvylation of human-type complex oligosaccharides would provide a novel method for glyco-bioengineering.

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Organizational Affiliation: 
• Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Fukuoka 812-8581, Japan.
Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Central-2, 1-1-1, Umezono, Tsukuba, Ibaraki 305-8568, Japan.
Department of Functional Glycomics, Life Science Research Center, Kagawa University, Miki-cho, Kagawa 761-0793, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 78.28 kDa 
• Atom Count: 5,324 
• Modeled Residue Count: 662 
• Deposited Residue Count: 696 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvyl transferase 1	A, B	348	Schizosaccharomyces pombe 972h-	Mutation(s): 0  Gene Names: pvg1, SPAC8F11.10c, SPACUNK4.18 EC: 2
UniProt
Find proteins for Q9UT27 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q9UT27  Go to UniProtKB:  Q9UT27

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free:  0.183 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.529	α = 90
b = 85.529	β = 90
c = 93.611	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
PHENIX	model building
Coot	model building
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-06-08 
Deposition Author(s): Kanekiyo, M., Yoritsune, K., Yoshinaga, S., Higuchi, Y., Takegawa, K., Kakuta, Y.

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Funding Organization	Location	Grant Number
a Grant-in-Aid for Scientific Research from the Ministry of Education, Science, and Culture of Japan	Japan	--

Revision History  

• Version 1.0: 2016-06-08
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Data collection, Derived calculations
• Version 1.2: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary