Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 220.12 kDa 
• Atom Count: 15474 
• Residue Count: 1898 
• Unique protein chains: 2

5E9T

Crystal structure of GtfA/B complex

• DOI: 10.2210/pdb5E9T/pdb

• Classification: TRANSFERASE/CHAPERONE
• Organism(s): Streptococcus gordonii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-10-15 Released: 2016-03-02 
• Deposition Author(s): Chen, Y., Rapoport, T.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.92 Å
• R-Value Free: 0.275 
• R-Value Work: 0.217 
• R-Value Observed: 0.220 

Literature

Mechanism of a cytosolic O-glycosyltransferase essential for the synthesis of a bacterial adhesion protein.

Chen, Y., Seepersaud, R., Bensing, B.A., Sullam, P.M., Rapoport, T.A.

(2016) Proc Natl Acad Sci U S A 113: E1190-E1199

• PubMed: 26884191 
• DOI: 10.1073/pnas.1600494113
• Primary Citation of Related Structures:  
  5E9T, 5E9U


• PubMed Abstract: 
  

O-glycosylation of Ser and Thr residues is an important process in all organisms, which is only poorly understood. Such modification is required for the export and function of adhesin proteins that mediate the attachment of pathogenic Gram-positive bacteria to host cells. Here, we have analyzed the mechanism by which the cytosolic O-glycosyltransferase GtfA/B of Streptococcus gordonii modifies the Ser/Thr-rich repeats of adhesin. The enzyme is a tetramer containing two molecules each of GtfA and GtfB. The two subunits have the same fold, but only GtfA contains an active site, whereas GtfB provides the primary binding site for adhesin. During a first phase of glycosylation, the conformation of GtfB is restrained by GtfA to bind substrate with unmodified Ser/Thr residues. In a slow second phase, GtfB recognizes residues that are already modified with N-acetylglucosamine, likely by converting into a relaxed conformation in which one interface with GtfA is broken. These results explain how the glycosyltransferase modifies a progressively changing substrate molecule.

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Organizational Affiliation: 

Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115; Department of Cell Biology, Harvard Medical School, Boston, MA 02115; [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase Gtf1	A, C	503	Streptococcus gordonii	Mutation(s): 1  Gene Names: gtf1, gtfA EC: 2.4.1
Find proteins for Q9AET5 (Streptococcus gordonii) Explore Q9AET5  Go to UniProtKB:  Q9AET5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase-stabilizing protein Gtf2	B, D	447	Streptococcus gordonii	Mutation(s): 0  Gene Names: gtf2, gtfB
Find proteins for Q79T00 (Streptococcus gordonii) Explore Q79T00  Go to UniProtKB:  Q79T00

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.92 Å
• R-Value Free: 0.275 
• R-Value Work: 0.217 
• R-Value Observed: 0.220 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.93	α = 90
b = 196.41	β = 90
c = 220.86	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-10-15 
• Released Date: 2016-03-02 
Deposition Author(s): Chen, Y., Rapoport, T.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM052586
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History 

• Version 1.0: 2016-03-02
  Type: Initial release
  
• Version 1.1: 2016-03-16
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.3: 2019-11-20
  Changes: Author supporting evidence
• Version 1.4: 2020-10-21
  Changes: Data collection