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)

Macromolecule Content

• Total Structure Weight: 96.96 kDa 
• Atom Count: 6995 
• Modelled Residue Count: 777 
• Deposited Residue Count: 812 
• Unique protein chains: 1

5GVV

Crystal structure of the glycosyltransferase GlyE in Streptococcus pneumoniae TIGR4

• PDB DOI: 10.2210/pdb5GVV/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-09-07 Released: 2017-03-01 
• Deposition Author(s): Jiang, Y.L., Jin, H., Zhao, R.L., Yang, H.B., Chen, Y., Zhou, C.Z.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.257 
• R-Value Work: 0.204 
• R-Value Observed: 0.207 

Literature

Defining the enzymatic pathway for polymorphic O-glycosylation of the pneumococcal serine-rich repeat protein PsrP.

Jiang, Y.L., Jin, H., Yang, H.B., Zhao, R.L., Wang, S., Chen, Y., Zhou, C.Z.

(2017) J Biol Chem 292: 6213-6224

• PubMed: 28246170 
• DOI: 10.1074/jbc.M116.770446
• Primary Citation of Related Structures:  
  5GVV, 5GVW


• PubMed Abstract: 
  

Protein O -glycosylation is an important post-translational modification in all organisms, but deciphering the specific functions of these glycans is difficult due to their structural complexity. Understanding the glycosylation of mucin-like proteins presents a particular challenge as they are modified numerous times with both the enzymes involved and the glycosylation patterns being poorly understood. Here we systematically explored the O -glycosylation pathway of a mucin-like serine-rich repeat protein PsrP from the human pathogen Streptococcus pneumoniae TIGR4. Previous works have assigned the function of 3 of the 10 glycosyltransferases thought to modify PsrP, GtfA/B, and Gtf3 as catalyzing the first two reactions to form a unified disaccharide core structure. We now use in vivo and in vitro glycosylation assays combined with hydrolytic activity assays to identify the glycosyltransferases capable of decorating this core structure in the third and fourth steps of glycosylation. Specifically, the full-length GlyE and GlyG proteins and the GlyD DUF1792 domain participate in both steps, whereas full-length GlyA and the GlyD GT8 domain catalyze only the fourth step. Incorporation of different sugars to the disaccharide core structure at multiple sites along the serine-rich repeats results in a highly polymorphic product. Furthermore, crystal structures of apo- and UDP-complexed GlyE combined with structural analyses reveal a novel Rossmann-fold "add-on" domain that we speculate to function as a universal module shared by GlyD, GlyE, and GlyA to forward the peptide acceptor from one enzyme to another. These findings define the complete glycosylation pathway of a bacterial glycoprotein and offer a testable hypothesis of how glycosyltransferase coordination facilitates glycan assembly.

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Organizational Affiliation: 

Key Laboratory of Structural Biology, Chinese Academy of Science, Hefei, Anhui 230027, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl transferase family 8	A, B [auth F]	406	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: gspA_4, ERS409372_01175, ERS515225_01083

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP	D [auth A], F	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
MN	C [auth A], E [auth F]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B [auth F]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.257 
• R-Value Work: 0.204 
• R-Value Observed: 0.207 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.17	α = 90
b = 88.21	β = 90
c = 128.36	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-09-07 
• Released Date: 2017-03-01 
Deposition Author(s): Jiang, Y.L., Jin, H., Zhao, R.L., Yang, H.B., Chen, Y., Zhou, C.Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31270760

Revision History  

• Version 1.0: 2017-03-01
  Type: Initial release
  
• Version 1.1: 2017-10-18
  Changes: Author supporting evidence
• Version 1.2: 2017-12-06
  Changes: Database references