6H40

High resolution structure of MeT1 from Mycobacterium hassiacum in complex with 3-methoxy-1,2-propanediol.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.120 
  • R-Value Work: 0.108 
  • R-Value Observed: 0.109 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Biosynthesis of mycobacterial methylmannose polysaccharides requires a unique 1-O-methyltransferase specific for 3-O-methylated mannosides.

Ripoll-Rozada, J.Costa, M.Manso, J.A.Maranha, A.Miranda, V.Sequeira, A.Ventura, M.R.Macedo-Ribeiro, S.Pereira, P.J.B.Empadinhas, N.

(2019) Proc Natl Acad Sci U S A 116: 835-844

  • DOI: https://doi.org/10.1073/pnas.1813450116
  • Primary Citation of Related Structures:  
    6G7D, 6G80, 6H40

  • PubMed Abstract: 

    Mycobacteria are a wide group of organisms that includes strict pathogens, such as Mycobacterium tuberculosis , as well as environmental species known as nontuberculous mycobacteria (NTM), some of which-namely Mycobacterium avium -are important opportunistic pathogens. In addition to a distinctive cell envelope mediating critical interactions with the host immune system and largely responsible for their formidable resistance to antimicrobials, mycobacteria synthesize rare intracellular polymethylated polysaccharides implicated in the modulation of fatty acid metabolism, thus critical players in cell envelope assembly. These are the 6- O -methylglucose lipopolysaccharides (MGLP) ubiquitously detected across the Mycobacterium genus, and the 3- O -methylmannose polysaccharides (MMP) identified only in NTM. The polymethylated nature of these polysaccharides renders the intervening methyltransferases essential for their optimal function. Although the knowledge of MGLP biogenesis is greater than that of MMP biosynthesis, the methyltransferases of both pathways remain uncharacterized. Here, we report the identification and characterization of a unique S -adenosyl-l-methionine-dependent sugar 1- O -methyltransferase (MeT1) from Mycobacterium hassiacum that specifically blocks the 1-OH position of 3,3'-di- O -methyl-4α-mannobiose, a probable early precursor of MMP, which we chemically synthesized. The high-resolution 3D structure of MeT1 in complex with its exhausted cofactor, S -adenosyl-l-homocysteine, together with mutagenesis studies and molecular docking simulations, unveiled the enzyme's reaction mechanism. The functional and structural properties of this unique sugar methyltransferase further our knowledge of MMP biosynthesis and provide important tools to dissect the role of MMP in NTM physiology and resilience.


  • Organizational Affiliation

    Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, 4200-135 Porto, Portugal.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methyltransferase domain protein231Mycolicibacterium hassiacum DSM 44199Mutation(s): 0 
Gene Names: C731_4163
UniProt
Find proteins for K5B7F3 (Mycolicibacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849))
Explore K5B7F3 
Go to UniProtKB:  K5B7F3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK5B7F3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
F [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
FW5
Query on FW5

Download Ideal Coordinates CCD File 
E [auth A](2~{S})-3-methoxypropane-1,2-diol
C4 H10 O3
PSJBSUHYCGQTHZ-BYPYZUCNSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
J [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.134α = 90
b = 113.134β = 90
c = 41.107γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
PortugalSFRH/BPD/108004/2015

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-01-23
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description