7VWS

Carbazole Prenyl Transferase LvqB4

PDB DOI: https://doi.org/10.2210/pdb7VWS/pdb

Classification: TRANSFERASE
Organism(s): Streptomyces sp.
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-11-11 Released: 2022-03-23
Deposition Author(s): Suemune, H., Nagata, R., Kuzuyama, T., Nagano, S.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free: 0.213
R-Value Work: 0.176
R-Value Observed: 0.178

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural Basis for the Prenylation Reaction of Carbazole-Containing Natural Products Catalyzed by Squalene Synthase-Like Enzymes.

Nagata, R., Suemune, H., Kobayashi, M., Shinada, T., Shin-Ya, K., Nishiyama, M., Hino, T., Sato, Y., Kuzuyama, T., Nagano, S.

(2022) Angew Chem Int Ed Engl 61: e202117430-e202117430

PubMed: 35235232 Search on PubMed
DOI: https://doi.org/10.1002/anie.202117430
Primary Citation of Related Structures:
7VWS, 7VWT

PubMed Abstract:
Some enzymes annotated as squalene synthase catalyze the prenylation of carbazole-3,4-quinone-containing substrates in bacterial secondary metabolism. Their reaction mechanisms remain unclear because of their low sequence similarity to well-characterized aromatic substrate prenyltransferases (PTs). We determined the crystal structures of the carbazole PTs, and these revealed that the overall structure is well superposed on those of squalene synthases. In contrast, the stacking interaction between the prenyl donor and acceptor substrates resembles those observed in aromatic substrate PTs. Structural and mutational analyses suggest that the Ile and Asp residues are essential for the hydrophobic and hydrophilic interactions with the carbazole-3,4-quinone moiety of the prenyl acceptor, respectively, and a deprotonation mechanism of an intermediary σ-complex involving a catalytic triad is proposed. Our results provide a structural basis for a new subclass of aromatic substrate PTs.

Organizational Affiliation

Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.

Macromolecule Content

Total Structure Weight: 83.32 kDa
Atom Count: 5,991
Modelled Residue Count: 643
Deposited Residue Count: 720
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LvqB4	A, B	360	Streptomyces sp.	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
83B (Subject of Investigation/LOI) Query on 83B Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B]	F [auth A], J [auth B]	[(3S)-3,7-dimethyloct-6-enyl] phosphono hydrogen phosphate C₁₀ H₂₂ O₇ P₂ MDPFRHMROKBMSH-JTQLQIEISA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
AO6 (Subject of Investigation/LOI) Query on AO6 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B]	E [auth A], I [auth B]	2-methyl-1-[(2R)-2-oxidanylpropyl]-9H-carbazole-3,4-dione C₁₆ H₁₅ N O₃ HADDOKGXXGGODW-MRVPVSSYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] 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 G [auth B] MOL2 format, chain H [auth B]	C [auth A], D [auth A], G [auth B], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B]