9PYM | pdb_00009pym

Cryo-EM structure of the isethionate TRAP transporter IseQM from Oleidesulfovibrio alaskensis with bound isethionate

PDB DOI: https://doi.org/10.2210/pdb9PYM/pdb
EM Map EMD-72036: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Oleidesulfovibrio alaskensis G20, Helicobacter pylori
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-08-07 Released: 2025-11-12
Deposition Author(s): Newton-Vesty, M.C., Davies, J.S., Dobson, R.C.J.
Funding Organization(s): Marsden Fund

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.98 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural basis of isethionate transport by a TRAP transporter from a sulfate-reducing bacterium.

Newton-Vesty, M.C., Scalise, M., Jamieson, S.A., Currie, M.J., Brown, H.G., Valimehr, S., Tillett, Z.D., Hall, K.R., Quan, S., Allison, J.R., Whitten, A.E., Panjikar, S., Indiveri, C., Hanssen, E., Mace, P.D., North, R.A., Dobson, R.C.J., Davies, J.S.

(2025) Structure

PubMed: 41197622 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2025.10.011
Primary Citation of Related Structures:
9PYM

PubMed Abstract:
Sulfate-reducing bacteria import organosulfur compounds from the environment for anaerobic respiration. They contribute to human disease and are problematic in industrial settings because they produce hydrogen sulfide. Here, we demonstrate how the sulfate-reducing bacterium Oleidesulfovibrio alaskensis imports isethionate, a common organosulfonate, using a tripartite ATP-independent periplasmic (TRAP) transporter (OaIsePQM). The cryo-EM structure of isethionate-bound OaIseQM to 2.98 Å resolution defines the substrate-binding site, two Na ⁺-binding sites, and a distinct fusion helix. Key residues within the OaIseQM substrate-binding site are identified using substitution and proteoliposome assays. Functional studies demonstrate that OaIseQM requires the substrate-binding protein (OaIseP) and a Na ⁺ gradient to drive transport. Modeling of the OaIsePQM complex supports that elevator-type conformational changes are involved in this unique coupled transport process. This work expands our knowledge of the transport of organosulfur compounds in bacteria and establishes OaIsePQM as a new model system for exploring the mechanism of TRAP transporters.

Organizational Affiliation

Biomolecular Interaction Centre, School of Biological Sciences, MacDiarmid Institute for Advanced Materials and Nanotechnology, University of Canterbury, Christchurch 8140, New Zealand; Australian Research Council (ARC) Centre for Cryo-Electron Microscopy of Membrane Proteins, Parkville, VIC 3052, Australia.

Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Via P. Bucci 4C, 87036 Arcavacata di Rende, Italy.

Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand.

Biomolecular Interaction Centre, School of Biological Sciences, MacDiarmid Institute for Advanced Materials and Nanotechnology, University of Canterbury, Christchurch 8140, New Zealand.

Biomolecular Interaction Centre, Maurice Wilkins Centre for Molecular Biodiscovery, and School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand.

Australian Centre for Neutron Scattering (ACNS), Australian Nuclear Science and Technology Organisation (ANSTO), Lucas Heights, NSW 2234, Australia.

Australian Synchrotron, ANSTO, Clayton, 800 Blackburn Road, VIC 3168, Australia; Department of Molecular Biology and Biochemistry, Monash University, Melbourne, VIC 3800, Australia.

Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Via P. Bucci 4C, 87036 Arcavacata di Rende, Italy; CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Via Amendola 122/O, 70126 Bari, Italy.

Australian Research Council (ARC) Centre for Cryo-Electron Microscopy of Membrane Proteins, Parkville, VIC 3052, Australia; Ian Holmes Imaging Centre, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3010, Australia; Biomolecular Interaction Centre, Maurice Wilkins Centre for Molecular Biodiscovery, and School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand.

School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia.

Biomolecular Interaction Centre, School of Biological Sciences, MacDiarmid Institute for Advanced Materials and Nanotechnology, University of Canterbury, Christchurch 8140, New Zealand; Australian Research Council (ARC) Centre for Cryo-Electron Microscopy of Membrane Proteins, Parkville, VIC 3052, Australia; Department of Biochemistry & Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia. Electronic address: renwick.dobson@canterbury.ac.nz.

Australian Research Council (ARC) Centre for Cryo-Electron Microscopy of Membrane Proteins, Parkville, VIC 3052, Australia; Computational and Structural Biology Division, Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia. Electronic address: j.davies@victorchang.edu.au.

Macromolecule Content

Total Structure Weight: 125.41 kDa
Atom Count: 5,517
Modeled Residue Count: 717
Deposited Residue Count: 1,150
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isethionate TRAP transporter permease protein DctMQ	A	635	Oleidesulfovibrio alaskensis G20	Mutation(s): 0 Gene Names: dctMQ, Dde_1274
UniProt
Find proteins for Q312S1 (Oleidesulfovibrio alaskensis (strain ATCC BAA-1058 / DSM 17464 / G20)) Explore Q312S1 Go to UniProtKB: Q312S1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q312S1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Megabody C7HopQ	B	515	Helicobacter pylori	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PTY Query on PTY Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A]	PHOSPHATIDYLETHANOLAMINE C₄₀ H₈₀ N O₈ P NJGIRBISCGPRPF-KXQOOQHDSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
8X3 (Subject of Investigation/LOI) Query on 8X3 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	2-hydroxyethylsulfonic acid C₂ H₆ O₄ S SUMDYPCJJOFFON-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]