3OKC | pdb_00003okc

Crystal structure of Corynebacterium glutamicum PimB' bound to GDP (orthorhombic crystal form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.236 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Acceptor substrate discrimination in phosphatidyl-myo-inositol mannoside synthesis: structural and mutational analysis of mannosyltransferase Corynebacterium glutamicum PimB'.

Batt, S.M.Jabeen, T.Mishra, A.K.Veerapen, N.Krumbach, K.Eggeling, L.Besra, G.S.Futterer, K.

(2010) J Biological Chem 285: 37741-37752

  • DOI: https://doi.org/10.1074/jbc.M110.165407
  • Primary Citation Related Structures: 
    3OKA, 3OKC, 3OKP

  • PubMed Abstract: 

    Long term survival of the pathogen Mycobacterium tuberculosis in humans is linked to the immunomodulatory potential of its complex cell wall glycolipids, which include the phosphatidylinositol mannoside (PIM) series as well as the related lipomannan and lipoarabinomannan glycoconjugates. PIM biosynthesis is initiated by a set of cytosolic α-mannosyltransferases, catalyzing glycosyl transfer from the activated saccharide donor GDP-α-D-mannopyranose to the acceptor phosphatidyl-myo-inositol (PI) in an ordered and regio-specific fashion. Herein, we report the crystal structure of mannosyltransferase Corynebacterium glutamicum PimB' in complex with nucleotide to a resolution of 2.0 Å. PimB' attaches mannosyl selectively to the 6-OH of the inositol moiety of PI. Two crystal forms and GDP- versus GDP-α-d-mannopyranose-bound complexes reveal flexibility of the nucleotide conformation as well as of the structural framework of the active site. Structural comparison, docking of the saccharide acceptor, and site-directed mutagenesis pin regio-selectivity to a conserved Asp residue in the N-terminal domain that forces presentation of the correct inositol hydroxyl to the saccharide donor.


  • Organizational Affiliation
    • School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 43.35 kDa 
  • Atom Count: 3,023 
  • Modeled Residue Count: 378 
  • Deposited Residue Count: 394 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GDP-mannose-dependent alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase394Corynebacterium glutamicumMutation(s): 0 
Gene Names: cg2400Cgl2186NCGL2106pimB
EC: 2.4.1.57 (PDB Primary Data), 2.4.1.346 (UniProt)
UniProt
Find proteins for Q8NNK8 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534))
Explore Q8NNK8 
Go to UniProtKB:  Q8NNK8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NNK8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / 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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.236 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.852α = 90
b = 86.4β = 90
c = 106.639γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description