9U8H | pdb_00009u8h

Deposited: 2025-03-26 Released: 2025-10-15
Deposition Author(s): Takahashi, Y.S., Kohga, H., Yamamoto, K., Takahashi, J.F., Tanaka, Y., Ichikawa, M., Miyazaki, R., Tsukazaki, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

(2025) FEBS Lett 599: 2377-2387

PubMed Abstract:
The bacterial phosphotransferase system (PTS) mediates the uptake of specific carbohydrates via IIC transporters. Here, we report the crystal and cryo-electron microscopy (cryo-EM) structures of Leminorella grimontii galactitol-specific PTS enzyme IIC component (LgGatC), which is implicated in D-xylose uptake and belongs to the ascorbate-galactitol (AG) superfamily of IIC proteins. These structures, determined in the presence and absence of D-xylose, capture the transporter in an outward-facing conformation. A homology model of an inward-facing state, constructed based on these structures, supports an elevator-like transport mechanism. These findings provide structural insights into substrate recognition by GatC and offer a framework for understanding sugar transport in PTS IIC proteins.

Organizational Affiliation

Graduate School of Science and Technology, Nara Institute of Science and Technology, Japan.

Macromolecule Content

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PTS galactitol transporter subunit IIC	A, B	471	Leminorella grimontii	Mutation(s): 0 Gene Names: SOASR030_34840
UniProt
Find proteins for A0AAV5N9B3 (Leminorella grimontii) Explore A0AAV5N9B3 Go to UniProtKB: A0AAV5N9B3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AAV5N9B3
Sequence Annotations Expand
Reference Sequence

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OLC Query on OLC Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	C [auth A] D [auth A] E [auth B] F [auth B] G [auth B] C [auth A], D [auth A], E [auth B], F [auth B], G [auth B], H [auth B]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B]