3ZF8 | pdb_00003zf8

Crystal structure of Saccharomyces cerevisiae Mnn9 in complex with GDP and Mn.

• PDB DOI: https://doi.org/10.2210/pdb3ZF8/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-12-10 Released: 2013-09-25 
• Deposition Author(s): Striebeck, A., Schuettelkopf, A.W., van Aalten, D.M.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.239 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Yeast Mnn9 is Both a Priming Glycosyltransferase and an Allosteric Activator of Mannan Biosynthesis.

Striebeck, A., Robinson, D.A., Schuettelkopf, A.W., Van Aalten, D.M.F.

(2013) Open Biol 3: 30022

• PubMed: 24026536 
• DOI: https://doi.org/10.1098/rsob.130022
• Primary Citation Related Structures: 
  3ZF8


• PubMed Abstract: 
  

  The fungal cell possesses an essential carbohydrate cell wall. The outer layer, mannan, is formed by mannoproteins carrying highly mannosylated O- and N-linked glycans. Yeast mannan biosynthesis is initiated by a Golgi-located complex (M-Pol I) of two GT-62 mannosyltransferases, Mnn9p and Van1p, that are conserved in fungal pathogens. Saccharomyces cerevisiae and Candida albicans mnn9 knockouts show an aberrant cell wall and increased antibiotic sensitivity, suggesting the enzyme is a potential drug target. Here, we present the structure of ScMnn9 in complex with GDP and Mn(2+), defining the fold and catalytic machinery of the GT-62 family. Compared with distantly related GT-78/GT-15 enzymes, ScMnn9 carries an unusual extension. Using a novel enzyme assay and site-directed mutagenesis, we identify conserved amino acids essential for ScMnn9 'priming' α-1,6-mannosyltransferase activity. Strikingly, both the presence of the ScMnn9 protein and its product, but not ScMnn9 catalytic activity, are required to activate subsequent ScVan1 processive α-1,6-mannosyltransferase activity in the M-Pol I complex. These results reveal the molecular basis of mannan synthesis and will aid development of inhibitors targeting this process.

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Organizational Affiliation: 
• Division of Molecular Microbiology, University of Dundee, Dundee DD1 5EH, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 35.54 kDa 
• Atom Count: 2,506 
• Modeled Residue Count: 288 
• Deposited Residue Count: 305 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MANNAN POLYMERASE COMPLEXES SUBUNIT MNN9	A	305	Saccharomyces cerevisiae S288C	Mutation(s): 1
UniProt
Find proteins for P39107 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P39107  Go to UniProtKB:  P39107

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.239 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.09	α = 90
b = 57.09	β = 90
c = 330.91	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-25 
Deposition Author(s): Striebeck, A., Schuettelkopf, A.W., van Aalten, D.M.F.

Revision History  

• Version 1.0: 2013-09-25
  Type: Initial release
  
• Version 1.1: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other