7XVJ

Crystal structure of CdpNPT in complex with harmol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

Starting Model: experimental
View more details

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

  • DOI: https://doi.org/10.1007/s11418-022-01635-0
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
HFI (Subject of Investigation/LOI)
Query on HFI

Download Ideal Coordinates CCD File 
M [auth D]1-methyl-9~{H}-pyrido[3,4-b]indol-7-ol
C12 H10 N2 O
SATMZMMKDDTOSQ-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.265α = 90
b = 158.669β = 90
c = 161.432γ = 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