6MIT

LptBFGC from Enterobacter cloacae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.280 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural basis of unidirectional export of lipopolysaccharide to the cell surface.

Owens, T.W.Taylor, R.J.Pahil, K.S.Bertani, B.R.Ruiz, N.Kruse, A.C.Kahne, D.

(2019) Nature 567: 550-553

  • DOI: 10.1038/s41586-019-1039-0
  • Primary Citation of Related Structures:  
    6MJP, 6MIT

  • PubMed Abstract: 
  • Gram-negative bacteria are surrounded by an inner cytoplasmic membrane and by an outer membrane, which serves as a protective barrier to limit entry of many antibiotics. The distinctive properties of the outer membrane are due to the presence of lipopolysaccharide 1 ...

    Gram-negative bacteria are surrounded by an inner cytoplasmic membrane and by an outer membrane, which serves as a protective barrier to limit entry of many antibiotics. The distinctive properties of the outer membrane are due to the presence of lipopolysaccharide 1 . This large glycolipid, which contains numerous sugars, is made in the cytoplasm; a complex of proteins forms a membrane-to-membrane bridge that mediates transport of lipopolysaccharide from the inner membrane to the cell surface 1 . The inner-membrane components of the protein bridge comprise an ATP-binding cassette transporter that powers transport, but how this transporter ensures unidirectional lipopolysaccharide movement across the bridge to the outer membrane is unknown 2 . Here we describe two crystal structures of a five-component inner-membrane complex that contains all the proteins required to extract lipopolysaccharide from the membrane and pass it to the protein bridge. Analysis of these structures, combined with biochemical and genetic experiments, identifies the path of lipopolysaccharide entry into the cavity of the transporter and up to the bridge. We also identify a protein gate that must open to allow movement of substrate from the cavity onto the bridge. Lipopolysaccharide entry into the cavity is ATP-independent, but ATP is required for lipopolysaccharide movement past the gate and onto the bridge. Our findings explain how the inner-membrane transport complex controls efficient unidirectional transport of lipopolysaccharide against its concentration gradient.


    Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA. kahne@chemistry.harvard.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lipopolysaccharide export system ATP-binding proteinA, B, F [auth D], G [auth E]241Enterobacter cloacae subsp. cloacae ATCC 13047Mutation(s): 0 
Gene Names: ECL_04583
Membrane Entity: Yes 
UniProt
Find proteins for A0A0H3CR83 (Enterobacter cloacae subsp. cloacae (strain ATCC 13047 / DSM 30054 / NBRC 13535 / NCTC 10005 / WDCM 00083 / NCDC 279-56))
Explore A0A0H3CR83 
Go to UniProtKB:  A0A0H3CR83
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Lipopolysaccharide export system protein LptCC, H195Enterobacter cloacae subsp. cloacae ATCC 13047Mutation(s): 0 
Gene Names: lptCECL_04581
Membrane Entity: Yes 
UniProt
Find proteins for A0A0H3CU18 (Enterobacter cloacae subsp. cloacae (strain ATCC 13047 / DSM 30054 / NBRC 13535 / NCTC 10005 / WDCM 00083 / NCDC 279-56))
Explore A0A0H3CU18 
Go to UniProtKB:  A0A0H3CU18
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
LPS export ABC transporter permease LptFD [auth F], I366Enterobacter cloacaeMutation(s): 0 
Gene Names: lptFCP904_11410ERS370009_01510CKO00_11140D1175_20330GJ694_21085
Membrane Entity: Yes 
UniProt
Find proteins for A0A421IFY4 (Enterobacter cloacae)
Explore A0A421IFY4 
Go to UniProtKB:  A0A421IFY4
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Lipopolysaccharide export system permease protein LptGE [auth G], J360Enterobacter cloacae subsp. cloacae ATCC 13047Mutation(s): 0 
Gene Names: ECL_04592
Membrane Entity: Yes 
UniProt
Find proteins for A0A0H3CQA2 (Enterobacter cloacae subsp. cloacae (strain ATCC 13047 / DSM 30054 / NBRC 13535 / NCTC 10005 / WDCM 00083 / NCDC 279-56))
Explore A0A0H3CQA2 
Go to UniProtKB:  A0A0H3CQA2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NOV (Subject of Investigation/LOI)
Query on NOV

Download Ideal Coordinates CCD File 
U [auth E]NOVOBIOCIN
C31 H36 N2 O11
YJQPYGGHQPGBLI-KGSXXDOSSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
K [auth A] , L [auth A] , N [auth B] , O [auth F] , P [auth G] , Q [auth G] , R [auth G] , S [auth D] , 
K [auth A],  L [auth A],  N [auth B],  O [auth F],  P [auth G],  Q [auth G],  R [auth G],  S [auth D],  T [auth E],  V [auth J],  W [auth J]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
M [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.280 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.427α = 90
b = 156.984β = 90
c = 295.518γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 GM066174
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI081059

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-27
    Type: Initial release
  • Version 1.1: 2019-04-03
    Changes: Data collection, Database references
  • Version 1.2: 2019-04-10
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.4: 2020-10-21
    Changes: Data collection