9GE7 | pdb_00009ge7

Structure of E. coli YbbAP with bound ATP analogue


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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This is version 1.1 of the entry. See complete history


Literature

Structural characterization of the YbbAP-TesA ABC transporter identifies it as a lipid hydrolase complex that extracts hydrophobic compounds from the bacterial inner membrane.

McAndrew, M.B.L.Cook, J.Gill, A.Sahoo, K.Thomas, C.Stansfeld, P.J.Crow, A.

(2025) PLoS Biol 23: e3003427-e3003427

  • DOI: https://doi.org/10.1371/journal.pbio.3003427
  • Primary Citation Related Structures: 
    9GE6, 9GE7, 9GE8

  • PubMed Abstract: 

    Type VII ABC transporters are ATP-powered membrane protein complexes that drive key biological processes in the bacterial cell envelope. In Escherichia coli, three of the four Type VII ABC systems have been extensively characterized, including: the FtsEX-EnvC cell division complex, the LolCDE-LolA lipoprotein trafficking machinery, and the MacAB-TolC efflux pump. Here we describe a fourth E. coli Type VII ABC system, YbbAP-TesA, which combines a Type VII ABC transporter with a multifunctional hydrolytic enzyme. Structures of the complete YbbAP-TesA complex, and of YbbAP with and without bound ATP analogues, capture implied long-range transmembrane conformational changes that are the hallmark of this ABC superfamily's mechanotransmission mechanism. We further show that YbbAP-TesA can hydrolyze a variety of ester and thioester substrates and experimentally confirm a constellation of active site residues in TesA. Our data suggests YbbAP has a role in extracting hydrophobic molecules from the inner membrane and presenting these to TesA for hydrolysis. The work extends collective knowledge of the remarkable diversity of the ABC superfamily and establishes a new function for Type VII ABC transporters in bacterial cells.


  • Organizational Affiliation
    • School of Life Sciences, University of Warwick, Coventry, United Kingdom.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized ABC transporter permease YbbP804Escherichia coli K-12Mutation(s): 0 
Gene Names: ybbPb0496JW0485
UniProt
Find proteins for P77504 (Escherichia coli (strain K12))
Explore P77504 
Go to UniProtKB:  P77504
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP77504
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized ABC transporter ATP-binding protein YbbA
B, C
242Escherichia coli K-12Mutation(s): 0 
Gene Names: ybbAb0495JW0484
UniProt
Find proteins for P0A9T8 (Escherichia coli (strain K12))
Explore P0A9T8 
Go to UniProtKB:  P0A9T8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A9T8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION5

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/N014294/1

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-28
    Type: Initial release
  • Version 1.1: 2026-04-22
    Changes: Data collection, Database references