7XVJ | pdb_00007xvj

Crystal structure of CdpNPT in complex with harmol

PDB DOI: https://doi.org/10.2210/pdb7XVJ/pdb

Classification: TRANSFERASE
Organism(s): Aspergillus fumigatus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-05-24 Released: 2023-04-05
Deposition Author(s): Nakashima, Y., Morita, H.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.223 (Depositor), 0.220 (DCC)
R-Value Work:
0.184 (Depositor), 0.182 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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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

Enzymatic formation of a prenyl beta-carboline by a fungal indole prenyltransferase.

Hamdy, S.A., Kodama, T., Nakashima, Y., Han, X., Matsui, T., Morita, H.

(2022) J Nat Med 76: 873-879

PubMed: 35767141 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1007/s11418-022-01635-0
Primary Citation Related Structures:
7XVJ

PubMed Abstract:
CdpNPT from Aspergillus fumigatus is a fungal indole prenyltransferase (IPT) with remarkable substrate promiscuity to generate prenylated compounds. Our first investigation of the catalytic potential of CdpNPT against a β-carboline, harmol (1), revealed that the enzyme also accepts 1 as the prenyl acceptor with dimethylallyl diphosphate (DMAPP) as the prenyl donor and selectively prenylates the C-6 position of 1 by the "regular-type" dimethylallylation to produce 6-(3-dimethylallyl)harmol (2). Furthermore, our X-ray crystal structure analysis of the C-His ₆-tagged CdpNPT (38-440) truncated mutant complexed with 1 and docking studies of DMAPP to the crystal structure of the CdpNPT (38-440) mutant suggested that CdpNPT could employ the two-step prenylation system to produce 2.

Organizational Affiliation

Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo, 11562, Egypt.

Macromolecule Content

Total Structure Weight: 185.43 kDa
Atom Count: 13,543
Modeled Residue Count: 1,584
Deposited Residue Count: 1,616
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic dipeptide N-prenyltransferase	A, B, C, D	404	Aspergillus fumigatus	Mutation(s): 0 Gene Names: cdpNPT EC: 3.4.11.17 (UniProt), 2.5.1 (UniProt)
UniProt
Find proteins for D1D8L6 (Aspergillus fumigatus) Explore D1D8L6 Go to UniProtKB: D1D8L6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D1D8L6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HFI (Subject of Investigation/LOI) Query on HFI Download:Ideal Coordinates CCD File SDF format, chain M [auth D] MOL2 format, chain M [auth D] mmCIF format, chain M [auth D]	M [auth D]	1-methyl-9~{H}-pyrido[3,4-b]indol-7-ol C₁₂ H₁₀ N₂ O SATMZMMKDDTOSQ-UHFFFAOYSA-N		Interactions Focus chain M [auth D] Interactions & Density Focus chain M [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain L [auth D] SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain I [auth C] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth D] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth D] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B]	E [auth A] F [auth A] G [auth B] H [auth B] I [auth C] E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D]