7Y3V | pdb_00007y3v

Crystal structure of CdpNPT in complex with harmane


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 
    0.236 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.237 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7Y3V

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Catalytic potential of a fungal indole prenyltransferase toward beta-carbolines, harmine and harman, and their prenylation effects on antibacterial activity.

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

(2022) J Biosci Bioeng 134: 311-317

  • DOI: https://doi.org/10.1016/j.jbiosc.2022.07.004
  • Primary Citation Related Structures: 
    7Y3V

  • PubMed Abstract: 

    The prenylation of compounds has attracted much attention, since it often adds bioactivity to non-prenylated compounds. We employed an enzyme assay with CdpNPT, an indole prenyltransferase from Aspergillus fumigatus with two naturally occurring β-carbolines, harmine (3) and harman (4) as prenyl acceptors, in the presence of dimethylallyl diphosphate (DMAPP) as the prenyl donor. The enzyme accepted these two prenyl acceptor substrates to produce 6-(3',3'-dimethylallyl)harmine (5) from 3 and 9-(3',3'-dimethylallyl)harman (6) and 6-(3',3'-dimethylallyl)harman (7) from 4. The X-ray crystal structure analysis of the CdpNPT (38-440) truncated mutant complexed with 4, and docking simulation studies of DMAPP to the crystal structure of the CdpNPT (38-440) mutant, suggested that CdpNPT could employ the two-step prenylation mechanism to produce 7, while the enzyme produced 6 with either one- or two-step prenylation mechanisms. Furthermore, the antibacterial assays revealed that the 3',3'-dimethylallylation of 3 and 4, as well as harmol (1), at C-6 enhanced the activities against Staphylococcus aureus and Bacillus subtilis.


  • Organizational Affiliation
    • Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo 11562, Egypt; Institute of Natural Medicine, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.

Macromolecule Content 

  • Total Structure Weight: 185.41 kDa 
  • Atom Count: 12,965 
  • Modeled Residue Count: 1,579 
  • Deposited Residue Count: 1,616 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cyclic dipeptide N-prenyltransferase
A, B, C, D
404Aspergillus fumigatusMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD1D8L6
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CN9
(Subject of Investigation/LOI)

Query on CN9



Download:Ideal Coordinates CCD File
G [auth A]1-methyl-9H-pyrido[3,4-b]indole
C12 H10 N2
PSFDQSOCUJVVGF-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
H [auth B]
I [auth B]
J [auth C]
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth C],
K [auth C],
L [auth D],
M [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free:  0.236 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.237 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.655α = 90
b = 157.237β = 90
c = 161.897γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan22H02777
Japan Society for the Promotion of Science (JSPS)Japan22K15303

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-05
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description