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 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.98 kDa 
• Atom Count: 2258 
• Modelled Residue Count: 284 
• Deposited Residue Count: 406 
• Unique protein chains: 1

3PTY

Crystal structure of the C-terminal extracellular domain of Mycobacterium tuberculosis EmbC

• PDB DOI: 10.2210/pdb3PTY/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-12-03 Released: 2010-12-15 
• Deposition Author(s): Alderwick, L.J., Besra, G.S., Futterer, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.207 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 

Literature

The C-Terminal Domain of the Arabinosyltransferase Mycobacterium tuberculosis EmbC Is a Lectin-Like Carbohydrate Binding Module.

Alderwick, L.J., Lloyd, G.S., Ghadbane, H., May, J.W., Bhatt, A., Eggeling, L., Futterer, K., Besra, G.S.

(2011) PLoS Pathog 7: e1001299-e1001299

• PubMed: 21383969 
• DOI: 10.1371/journal.ppat.1001299
• Primary Citation of Related Structures:  
  3PTY


• PubMed Abstract: 
  

The D-arabinan-containing polymers arabinogalactan (AG) and lipoarabinomannan (LAM) are essential components of the unique cell envelope of the pathogen Mycobacterium tuberculosis. Biosynthesis of AG and LAM involves a series of membrane-embedded arabinofuranosyl (Araf) transferases whose structures are largely uncharacterised, despite the fact that several of them are pharmacological targets of ethambutol, a frontline drug in tuberculosis therapy. Herein, we present the crystal structure of the C-terminal hydrophilic domain of the ethambutol-sensitive Araf transferase M. tuberculosis EmbC, which is essential for LAM synthesis. The structure of the C-terminal domain of EmbC (EmbC(CT)) encompasses two sub-domains of different folds, of which subdomain II shows distinct similarity to lectin-like carbohydrate-binding modules (CBM). Co-crystallisation with a cell wall-derived di-arabinoside acceptor analogue and structural comparison with ligand-bound CBMs suggest that EmbC(CT) contains two separate carbohydrate binding sites, associated with subdomains I and II, respectively. Single-residue substitution of conserved tryptophan residues (Trp868, Trp985) at these respective sites inhibited EmbC-catalysed extension of LAM. The same substitutions differentially abrogated binding of di- and penta-arabinofuranoside acceptor analogues to EmbC(CT), linking the loss of activity to compromised acceptor substrate binding, indicating the presence of two separate carbohydrate binding sites, and demonstrating that subdomain II indeed functions as a carbohydrate-binding module. This work provides the first step towards unravelling the structure and function of a GT-C-type glycosyltransferase that is essential in M. tuberculosis.

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Organizational Affiliation: 

School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arabinosyltransferase C	A	406	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: embC, MT3900, MTCY13D12.27, Rv3793 EC: 2.4.2
UniProt
Find proteins for P9WNL5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WNL5  Go to UniProtKB:  P9WNL5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AFO	B [auth A]	octyl alpha-D-arabinofuranoside C13 H26 O5 DULPXMOVQIYGDB-NDBYEHHHSA-N
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AFO	PDBBind:  3PTY	Kd: 3650 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.207 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.13	α = 90
b = 129.13	β = 90
c = 136.73	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
SHELXDE	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-12-03 
• Released Date: 2010-12-15 
Deposition Author(s): Alderwick, L.J., Besra, G.S., Futterer, K.

Revision History  

• Version 1.0: 2010-12-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations