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Structure paper

TitleStructure and mechanism of a tripartite ATP-independent periplasmic TRAP transporter.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 1120, Year 2023
Publish dateFeb 27, 2023
AuthorsJames S Davies / Michael J Currie / Rachel A North / Mariafrancesca Scalise / Joshua D Wright / Jack M Copping / Daniela M Remus / Ashutosh Gulati / Dustin R Morado / Sam A Jamieson / Michael C Newton-Vesty / Gayan S Abeysekera / Subramanian Ramaswamy / Rosmarie Friemann / Soichi Wakatsuki / Jane R Allison / Cesare Indiveri / David Drew / Peter D Mace / Renwick C J Dobson /
PubMed AbstractIn bacteria and archaea, tripartite ATP-independent periplasmic (TRAP) transporters uptake essential nutrients. TRAP transporters receive their substrates via a secreted soluble substrate-binding ...In bacteria and archaea, tripartite ATP-independent periplasmic (TRAP) transporters uptake essential nutrients. TRAP transporters receive their substrates via a secreted soluble substrate-binding protein. How a sodium ion-driven secondary active transporter is strictly coupled to a substrate-binding protein is poorly understood. Here we report the cryo-EM structure of the sialic acid TRAP transporter SiaQM from Photobacterium profundum at 2.97 Å resolution. SiaM comprises a "transport" domain and a "scaffold" domain, with the transport domain consisting of helical hairpins as seen in the sodium ion-coupled elevator transporter VcINDY. The SiaQ protein forms intimate contacts with SiaM to extend the size of the scaffold domain, suggesting that TRAP transporters may operate as monomers, rather than the typically observed oligomers for elevator-type transporters. We identify the Na and sialic acid binding sites in SiaM and demonstrate a strict dependence on the substrate-binding protein SiaP for uptake. We report the SiaP crystal structure that, together with docking studies, suggest the molecular basis for how sialic acid is delivered to the SiaQM transporter complex. We thus propose a model for substrate transport by TRAP proteins, which we describe herein as an 'elevator-with-an-operator' mechanism.
External linksNat Commun / PubMed:36849793 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.04 - 3.03 Å
Structure data

13968

7qha

EMDB-13968, PDB-7qha:
Cryo-EM structure of the Tripartite ATP-independent Periplasmic (TRAP) transporter SiaQM from Photobacterium profundum in amphipol
Method: EM (single particle) / Resolution: 2.97 Å

15775

8b01

EMDB-15775, PDB-8b01:
Cryo-EM structure of the Tripartite ATP-independent Periplasmic (TRAP) transporter SiaQM from Photobacterium profundum in a nanodisc
Method: EM (single particle) / Resolution: 3.03 Å

PDB-7t3e:
Structure of the sialic acid bound Tripartite ATP-independent Periplasmic (TRAP) periplasmic component SiaP from Photobacterium profundum
Method: X-RAY DIFFRACTION / Resolution: 1.04 Å

Chemicals

ChemComp-NA:
Unknown entry

ChemComp-SLB:
N-acetyl-beta-neuraminic acid / N-Acetylneuraminic acid

ChemComp-SO4:
SULFATE ION / Sulfate

ChemComp-HOH:
WATER / Water

ChemComp-OCT:
N-OCTANE / Octane

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM / Phosphatidylethanolamine

ChemComp-TWT:
DOCOSANE / Higher alkanes

ChemComp-D10:
DECANE / Decane

ChemComp-TRD:
TRIDECANE / Tridecane

ChemComp-HEX:
HEXANE / Hexane

Source
  • photobacterium profundum (bacteria)
  • helicobacter pylori (bacteria)
  • photobacterium profundum ss9 (bacteria)
  • synthetic construct (others)
KeywordsTRANSPORT PROTEIN / TRAP / elevator / secondary transporter / sialic acid / Periplasmic SBP / TRAP transporter

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