2BYO | pdb_00002byo

Crystal structure of Mycobacterium tuberculosis lipoprotein LppX (Rv2945c)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.224 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Lppx is a Lipoprotein Required for the Translocation of Phthiocerol Dimycocerosates to the Surface of Mycobacterium Tuberculosis.

Sulzenbacher, G.Canaan, S.Bordat, Y.Neyrolles, O.Stadthagen, G.Roig-Zamboni, V.Rauzier, J.Maurin, D.Laval, F.Daffe, M.Cambillau, C.Gicquel, B.Bourne, Y.Jackson, M.

(2006) EMBO J 25: 1436

  • DOI: https://doi.org/10.1038/sj.emboj.7601048
  • Primary Citation Related Structures: 
    2BYO

  • PubMed Abstract: 

    Cell envelope lipids play an important role in the pathogenicity of mycobacteria, but the mechanisms by which they are transported to the outer membrane of these prokaryotes are largely unknown. Here, we provide evidence that LppX is a lipoprotein required for the translocation of complex lipids, the phthiocerol dimycocerosates (DIM), to the outer membrane of Mycobacterium tuberculosis. Abolition of DIM transport following disruption of the lppX gene is accompanied by an important attenuation of the virulence of the tubercle bacillus. The crystal structure of LppX unveils an U-shaped beta-half-barrel dominated by a large hydrophobic cavity suitable to accommodate a single DIM molecule. LppX shares a similar fold with the periplasmic molecular chaperone LolA and the outer membrane lipoprotein LolB, which are involved in the localization of lipoproteins to the outer membrane of Gram-negative bacteria. Based on the structure and although an indirect participation of LppX in DIM transport cannot yet be ruled out, we propose LppX to be the first characterized member of a family of structurally related lipoproteins that carry lipophilic molecules across the mycobacterial cell envelope.


  • Organizational Affiliation
    • AFMB, CNRS UMR 6098, Marseille Cedex, France.

Macromolecule Content 

  • Total Structure Weight: 23.13 kDa 
  • Atom Count: 1,565 
  • Modeled Residue Count: 183 
  • Deposited Residue Count: 207 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LIPOPROTEIN LPPX207Mycobacterium tuberculosis H37RvMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P9WK65 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WK65 
Go to UniProtKB:  P9WK65
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WK65
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HXA

Query on HXA



Download:Ideal Coordinates CCD File
I [auth A]DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID
C22 H32 O2
MBMBGCFOFBJSGT-KUBAVDMBSA-N
LNL

Query on LNL



Download:Ideal Coordinates CCD File
J [auth A],
K [auth A]
ALPHA-LINOLENIC ACID
C18 H30 O2
DTOSIQBPPRVQHS-PDBXOOCHSA-N
MLT

Query on MLT



Download:Ideal Coordinates CCD File
M [auth A]D-MALATE
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
OAA

Query on OAA



Download:Ideal Coordinates CCD File
L [auth A]OXALOACETATE ION
C4 H3 O5
KHPXUQMNIQBQEV-UHFFFAOYSA-M
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
H [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.224 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.257α = 90
b = 54.257β = 90
c = 269.983γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata 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: 2006-03-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Refinement description, Version format compliance
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other