8HZZ

GuApiGT (UGT79B74)

PDB DOI: https://doi.org/10.2210/pdb8HZZ/pdb

Classification: PLANT PROTEIN
Organism(s): Glycyrrhiza uralensis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-01-10 Released: 2023-09-20
Deposition Author(s): Wang, H.T., Wang, Z.L., Li, F.D., Ye, M.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.237
R-Value Work: 0.191
R-Value Observed: 0.194

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

This is version 1.2 of the entry. See complete history.

Literature

Insights into the missing apiosylation step in flavonoid apiosides biosynthesis of Leguminosae plants.

Wang, H.T., Wang, Z.L., Chen, K., Yao, M.J., Zhang, M., Wang, R.S., Zhang, J.H., Agren, H., Li, F.D., Li, J., Qiao, X., Ye, M.

(2023) Nat Commun 14: 6658-6658

PubMed: 37863881 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-023-42393-1
Primary Citation of Related Structures:
8HZZ, 8I0D, 8I0E

PubMed Abstract:
Apiose is a natural pentose containing an unusual branched-chain structure. Apiosides are bioactive natural products widely present in the plant kingdom. However, little is known on the key apiosylation reaction in the biosynthetic pathways of apiosides. In this work, we discover an apiosyltransferase GuApiGT from Glycyrrhiza uralensis. GuApiGT could efficiently catalyze 2″-O-apiosylation of flavonoid glycosides, and exhibits strict selectivity towards UDP-apiose. We further solve the crystal structure of GuApiGT, determine a key sugar-binding motif (RLGSDH) through structural analysis and theoretical calculations, and obtain mutants with altered sugar selectivity through protein engineering. Moreover, we discover 121 candidate apiosyltransferase genes from Leguminosae plants, and identify the functions of 4 enzymes. Finally, we introduce GuApiGT and its upstream genes into Nicotiana benthamiana, and complete de novo biosynthesis of a series of flavonoid apiosides. This work reports an efficient phenolic apiosyltransferase, and reveals mechanisms for its sugar donor selectivity.

Organizational Affiliation

State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China.

Macromolecule Content

Total Structure Weight: 102.28 kDa
Atom Count: 7,327
Modelled Residue Count: 898
Deposited Residue Count: 908
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
apiosyltransferase	A, B	454	Glycyrrhiza uralensis	Mutation(s): 0
UniProt
Find proteins for A0AA51Z2W4 (Glycyrrhiza uralensis) Explore A0AA51Z2W4 Go to UniProtKB: A0AA51Z2W4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0AA51Z2W4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]