6BUG

Crystal structure of a membrane protein, crystal form I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.27 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.290 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of a membrane-bound O-acyltransferase.

Ma, D.Wang, Z.Merrikh, C.N.Lang, K.S.Lu, P.Li, X.Merrikh, H.Rao, Z.Xu, W.

(2018) Nature 562: 286-290

  • DOI: https://doi.org/10.1038/s41586-018-0568-2
  • Primary Citation of Related Structures:  
    6BUG, 6BUH, 6BUI

  • PubMed Abstract: 

    Membrane-bound O-acyltransferases (MBOATs) are a superfamily of integral transmembrane enzymes that are found in all kingdoms of life 1 . In bacteria, MBOATs modify protective cell-surface polymers. In vertebrates, some MBOAT enzymes-such as acyl-coenzyme A:cholesterol acyltransferase and diacylglycerol acyltransferase 1-are responsible for lipid biosynthesis or phospholipid remodelling 2,3 . Other MBOATs, including porcupine, hedgehog acyltransferase and ghrelin acyltransferase, catalyse essential lipid modifications of secreted proteins such as Wnt, hedgehog and ghrelin, respectively 4-10 . Although many MBOAT proteins are important drug targets, little is known about their molecular architecture and functional mechanisms. Here we present crystal structures of DltB, an MBOAT responsible for the D-alanylation of cell-wall teichoic acid in Gram-positive bacteria 11-16 , both alone and in complex with the D-alanyl donor protein DltC. DltB contains a ring of 11 peripheral transmembrane helices, which shield a highly conserved extracellular structural funnel extending into the middle of the lipid bilayer. The conserved catalytic histidine residue is located at the bottom of this funnel and is connected to the intracellular DltC through a narrow tunnel. Mutation of either the catalytic histidine or the DltC-binding site of DltB abolishes the D-alanylation of lipoteichoic acid and sensitizes the Gram-positive bacterium Bacillus subtilis to cell-wall stress, which suggests cross-membrane catalysis involving the tunnel. Structure-guided sequence comparison among DltB and vertebrate MBOATs reveals a conserved structural core and suggests that MBOATs from different organisms have similar catalytic mechanisms. Our structures provide a template for understanding structure-function relationships in MBOATs and for developing therapeutic MBOAT inhibitors.


  • Organizational Affiliation

    Department of Biological Structure, University of Washington, Seattle, WA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-alanyl carrier proteinA,
C [auth B],
E
82Streptococcus thermophilusMutation(s): 0 
Gene Names: dltC
UniProt
Find proteins for Q5M4V3 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311))
Explore Q5M4V3 
Go to UniProtKB:  Q5M4V3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5M4V3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
D-alanyl transfer protein DltBB [auth C],
D,
F,
G
425Streptococcus thermophilusMutation(s): 0 
Gene Names: dltB
Membrane Entity: Yes 
UniProt
Find proteins for Q5M4V4 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311))
Explore Q5M4V4 
Go to UniProtKB:  Q5M4V4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5M4V4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A,
C [auth B],
E
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.27 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.290 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.713α = 90
b = 121.119β = 101.58
c = 126.529γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2018-10-17
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2018-10-24
    Changes: Data collection, Database references