Biological Assembly 1  

 3D View: Structure | Electron Density

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: 65.71 kDa 
• Atom Count: 3575 
• Modelled Residue Count: 446 
• Deposited Residue Count: 598 
• Unique protein chains: 1

3G2M

Crystal Structure of the Glycopeptide N-methyltransferase MtfA

• DOI: 10.2210/pdb3G2M/pdb

• Classification: TRANSFERASE
• Organism(s): Amycolatopsis orientalis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-31 Released: 2009-05-05 
• Deposition Author(s): Shi, R., Matte, A., Cygler, M., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.271 
• R-Value Work: 0.238 
• R-Value Observed: 0.239 

Literature

Structure and function of the glycopeptide N-methyltransferase MtfA, a tool for the biosynthesis of modified glycopeptide antibiotics.

Shi, R., Lamb, S.S., Zakeri, B., Proteau, A., Cui, Q., Sulea, T., Matte, A., Wright, G.D., Cygler, M.

(2009) Chem Biol 16: 401-410

• PubMed: 19389626 
• DOI: 10.1016/j.chembiol.2009.02.007
• Primary Citation of Related Structures:  
  3G2O, 3G2P, 3G2Q, 3G2M


• PubMed Abstract: 
  

There is a considerable interest in the modification of existing antibiotics to generate new antimicrobials. Glycopeptide antibiotics (GPAs) are effective against serious Gram-positive bacterial pathogens including methicillin-resistant Staphylococcus aureus. However, resistance to these antibiotics is becoming a serious problem requiring new strategies. We show that the Amycolatopsis orientalis (S)-adenosyl-L-methionine-dependent methyltransferase MtfA, from the vancomycin-class GPA chloroeremomycin biosynthetic pathway, catalyzes in vivo and in vitro methyl transfer to generate methylated GPA derivatives of the teicoplanin class. The crystal structure of MtfA complexed with (S)-adenosyl-L-methionine, (S)-adenosylhomocysteine, or sinefungin inhibitor, coupled with mutagenesis, identified His228 as a likely general base required for methyl transfer to the N terminus of the glycopeptide. Computational docking and molecular dynamics simulations were used to model binding of demethyl-vancomycin aglycone to MtfA. These results demonstrate its utility as a tool for engineering methylated analogs of GPAs.

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Organizational Affiliation: 

Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montréal, QC H3G 1Y6, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PCZA361.24	A, B	299	Amycolatopsis orientalis	Mutation(s): 0  Gene Names: mtfA
UniProt
Find proteins for O52805 (Amycolatopsis orientalis) Explore O52805  Go to UniProtKB:  O52805

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.271 
• R-Value Work: 0.238 
• R-Value Observed: 0.239 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.443	α = 90
b = 71.682	β = 103.02
c = 75.189	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-01-31 
• Released Date: 2009-05-05 
Deposition Author(s): Shi, R., Matte, A., Cygler, M., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)

Revision History  

• Version 1.0: 2009-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description