4N9W

Crystal structure of phosphatidyl mannosyltransferase PimA

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 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


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

  • DOI: 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 ...

    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: 

    Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528, Paris, France.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GDP-mannose-dependent alpha-(1-2)-phosphatidylinositol mannosyltransferaseA390Mycolicibacterium smegmatis MC2 155Mutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0QWG6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP
Download Ideal Coordinates CCD File 
B [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
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 = 37.507α = 90
b = 75.515β = 97.69
c = 59.326γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-12
    Type: Initial release
  • Version 1.1: 2015-06-10
    Changes: Database references