5AX7

yeast pyruvyltransferase Pvg1p


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • DOI: 10.1038/srep26349
  • Primary Citation of 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 ...

    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.


    Organizational Affiliation

    Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Fukuoka 812-8581, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyruvyl transferase 1 AB348Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: pvg1SPAC8F11.10cSPACUNK4.18
EC: 2
Find proteins for Q9UT27 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9UT27 
Go to UniProtKB:  Q9UT27
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.529α = 90
b = 85.529β = 90
c = 93.611γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
PHENIXmodel building
Cootmodel building
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
a Grant-in-Aid for Scientific Research from the Ministry of Education, Science, and Culture of JapanJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection, Derived calculations