4N9W

Crystal structure of phosphatidyl mannosyltransferase PimA

• PDB DOI: https://doi.org/10.2210/pdb4N9W/pdb

• Classification: TRANSFERASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2013-10-21 Released: 2014-11-12 
• Deposition Author(s): Giganti, D., Albesa-Jove, D., Bellinzoni, M., Guerin, M.E., Alzari, P.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.211 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 

Literature

Secondary structure reshuffling modulates glycosyltransferase function at the membrane.

Giganti, D., Albesa-Jove, D., Urresti, S., Rodrigo-Unzueta, A., Martinez, M.A., Comino, N., Barilone, N., Bellinzoni, M., Chenal, A., Guerin, M.E., Alzari, P.M.

(2015) Nat Chem Biol 11: 16-18

• PubMed: 25402770 
• DOI: https://doi.org/10.1038/nchembio.1694
• Primary Citation of Related Structures:  
  4N9W, 4NC9


• PubMed Abstract: 
  

  Secondary structure refolding is a key event in biology as it modulates the conformation of many proteins in the cell, generating functional or aberrant states. The crystal structures of mannosyltransferase PimA reveal an exceptional flexibility of the protein along the catalytic cycle, including β-strand-to-α-helix and α-helix-to-β-strand transitions. These structural changes modulate catalysis and are promoted by interactions of the protein with anionic phospholipids in the membrane.

---

Organizational Affiliation: 

1] Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528, Paris, France. [2] Unidad de Biofisica, Centro Mixto Consejo Superior de Investigaciones Cientificas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Leioa, Bizkaia, Spain. [3] Departamento de Bioquímica, Universidad del País Vasco, Spain.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 42.05 kDa 
• Atom Count: 2,816 
• Modelled Residue Count: 360 
• Deposited Residue Count: 390 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDP-mannose-dependent alpha-(1-2)-phosphatidylinositol mannosyltransferase	A	390	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: MSMEG_2935, MSMEI_2861, pimA EC: 2.4.1.57 (PDB Primary Data), 2.4.1.345 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for A0QWG6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QWG6  Go to UniProtKB:  A0QWG6

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
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.211 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.507	α = 90
b = 75.515	β = 97.69
c = 59.326	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-12 
Deposition Author(s): Giganti, D., Albesa-Jove, D., Bellinzoni, M., Guerin, M.E., Alzari, P.M.

Revision History  

• Version 1.0: 2014-11-12
  Type: Initial release
  
• Version 1.1: 2015-06-10
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations