Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 43.51 kDa 
• Atom Count: 3068 
• Modelled Residue Count: 378 
• Deposited Residue Count: 394 
• Unique protein chains: 1

3OKP

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

• PDB DOI: 10.2210/pdb3OKP/pdb

• Classification: TRANSFERASE
• Organism(s): Corynebacterium glutamicum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-08-25 Released: 2010-09-15 
• Deposition Author(s): Batt, S.M., Jabeen, T., Besra, G.S., Futterer, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.232 
• R-Value Work: 0.203 
• R-Value Observed: 0.204 

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 Biol Chem 285: 37741-37752

• PubMed: 20843801 
• DOI: 10.1074/jbc.M110.165407
• Primary Citation of 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDP-mannose-dependent alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase	A	394	Corynebacterium glutamicum	Mutation(s): 0  Gene Names: cg2400, Cgl2186, NCGL2106, pimB 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 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025)) Explore Q8NNK8  Go to UniProtKB:  Q8NNK8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDD	B [auth A]	GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE C16 H25 N5 O16 P2 MVMSCBBUIHUTGJ-GDJBGNAASA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GDD	Binding MOAD:  3OKP	Kd: 1.90e+4 (nM) from 1 assay(s)
	PDBBind:  3OKP	Kd: 1.90e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.232 
• R-Value Work: 0.203 
• R-Value Observed: 0.204 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.746	α = 90
b = 87.002	β = 90
c = 106.895	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-08-25 
• Released Date: 2010-09-15 
Deposition Author(s): Batt, S.M., Jabeen, T., Besra, G.S., Futterer, K.

Revision History  

• Version 1.0: 2010-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance