6TQF

The structure of ABC transporter Rv1819c in AMP-PNP bound state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A mycobacterial ABC transporter mediates the uptake of hydrophilic compounds.

Rempel, S.Gati, C.Nijland, M.Thangaratnarajah, C.Karyolaimos, A.de Gier, J.W.Guskov, A.Slotboom, D.J.

(2020) Nature 580: 409-412

  • DOI: https://doi.org/10.1038/s41586-020-2072-8
  • Primary Citation of Related Structures:  
    6TQE, 6TQF

  • PubMed Abstract: 

    Mycobacterium tuberculosis (Mtb) is an obligate human pathogen and the causative agent of tuberculosis 1-3 . Although Mtb can synthesize vitamin B 12 (cobalamin) de novo, uptake of cobalamin has been linked to pathogenesis of tuberculosis 2 . Mtb does not encode any characterized cobalamin transporter 4-6 ; however, the gene rv1819c was found to be essential for uptake of cobalamin 1 . This result is difficult to reconcile with the original annotation of Rv1819c as a protein implicated in the transport of antimicrobial peptides such as bleomycin 7 . In addition, uptake of cobalamin seems inconsistent with the amino acid sequence, which suggests that Rv1819c has a bacterial ATP-binding cassette (ABC)-exporter fold 1 . Here, we present structures of Rv1819c, which reveal that the protein indeed contains the ABC-exporter fold, as well as a large water-filled cavity of about 7,700 Å 3 , which enables the protein to transport the unrelated hydrophilic compounds bleomycin and cobalamin. On the basis of these structures, we propose that Rv1819c is a multi-solute transporter for hydrophilic molecules, analogous to the multidrug exporters of the ABC transporter family, which pump out structurally diverse hydrophobic compounds from cells 8-11 .


  • Organizational Affiliation

    Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ABC transporter ATP-binding protein/permease
A, B
647Mycobacterium tuberculosisMutation(s): 1 
Gene Names: 
Membrane Entity: Yes 
UniProt
Find proteins for P9WQI9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WQI9 
Go to UniProtKB:  P9WQI9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WQI9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMT
Query on LMT

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
ANP
Query on ANP

Download Ideal Coordinates CCD File 
I [auth A],
P [auth B]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A],
O [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-01
    Type: Initial release
  • Version 1.1: 2020-04-29
    Changes: Database references
  • Version 1.2: 2021-02-10
    Changes: Derived calculations