9GPH | pdb_00009gph

Teth514_1788 1,2-beta-oligomannan phosphorylase in complex with mannose (-1) and phosphate

PDB DOI: https://doi.org/10.2210/pdb9GPH/pdb

Classification: CARBOHYDRATE
Organism(s): Thermoanaerobacter sp. X514
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-09-07 Released: 2025-09-17
Deposition Author(s): Cioci, G., Durand, J., Veronese-Potocki, G., Ladeveze, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.216 (Depositor), 0.225 (DCC)
R-Value Work:
0.192 (Depositor), 0.203 (DCC)

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.

Literature

Dual-Activity Mannosyltransferase Phosphorylases in Family 130 of Glycoside Hydrolases.

Ladeveze, S., Tarquis, L., Cioci, G., Guieysse, D., Durand, J., Faure, R., Li, A., Esque, J., Vivier, M., Malbert, Y., Laville, E., Potocki-Veronese, G.

(2026) ACS Catal 16: 1211-1223

PubMed: 41561435 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acscatal.5c06782
Primary Citation Related Structures:
9EQQ, 9FJ8, 9GPH

PubMed Abstract:
We discovered that certain mannoside-active enzymes from family GH130 possess both glycoside phosphorylase (GP) and weak glycosyltransferase (GT) activities. This dual activity was observed only in glycoside phosphorylases acting on β-(1,2)- and β-(1,3)-mannosides, being absent in β-(1,4)-mannoside phosphorylases. We provide several three-dimensional (3D) structures of β-(1,2)-mannosyltransferase phosphorylases Uhgb_MS (identified from the human gut microbiome (subfamily GH130_4)) and Teth514_1788 (from Thermoanaerobacter sp. X514 (subfamily GH130_6)) and analyzed GT/GP partitioning among enzymes acting on d-mannosides. Structural analysis and mutagenesis of Uhgb_MS allowed us to show that loop L2 folding, as well as nucleotide and phosphate binding residues (P206, N211, R242) at the location of the common structural phosphate of αMan1P and GDP-Man, is an important structural element of bifunctionality in GH130.

Organizational Affiliation

TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France.

Macromolecule Content

Total Structure Weight: 141.25 kDa
Atom Count: 10,665
Modeled Residue Count: 1,202
Deposited Residue Count: 1,212
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1,2-beta-oligomannan phosphorylase	A, B, C, D	303	Thermoanaerobacter sp. X514	Mutation(s): 0 Gene Names: Teth514_1788 EC: 2.4.1.340
UniProt
Find proteins for B0K2C2 (Thermoanaerobacter sp. (strain X514)) Explore B0K2C2 Go to UniProtKB: B0K2C2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B0K2C2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MAN (Subject of Investigation/LOI) Query on MAN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain N [auth C] SDF format, chain R [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D]	F [auth A], I [auth B], N [auth C], R [auth D]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain R [auth D]
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D]	E [auth A], H [auth B], M [auth C], Q [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain M [auth C] Focus chain Q [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain S [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D]	G [auth A] J [auth B] K [auth B] L [auth B] O [auth C] G [auth A], J [auth B], K [auth B], L [auth B], O [auth C], P [auth C], S [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D]