4E0U

Crystal structure of CdpNPT in complex with thiolodiphosphate and (S)-benzodiazependione


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.229 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 0MVClick on this verticalbar to view detailsBest fitted PISClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Structure and catalytic mechanism of a cyclic dipeptide prenyltransferase with broad substrate promiscuity.

Schuller, J.M.Zocher, G.Liebhold, M.Xie, X.Stahl, M.Li, S.M.Stehle, T.

(2012) J Mol Biol 422: 87-99

  • DOI: https://doi.org/10.1016/j.jmb.2012.05.033
  • Primary Citation of Related Structures:  
    4E0T, 4E0U

  • PubMed Abstract: 

    Fungal indole prenyltransferases (PTs) typically act on specific substrates, and they are able to prenylate their target compounds with remarkably high regio- and stereoselectivity. Similar to several indole PTs characterized to date, the cyclic dipeptide N-prenyltransferase (CdpNPT) is able to prenylate a range of diverse substrates, thus exhibiting an unusually broad substrate promiscuity. To define the structural basis for this promiscuity, we have determined crystal structures of unliganded CdpNPT and of a ternary complex of CdpNPT bound to (S)-benzodiazepinedione and thiolodiphosphate. Analysis of the structures reveals a limited number of specific interactions with (S)-benzodiazepinedione, which projects into a largely hydrophobic surface. This surface can also accommodate other substrates, explaining the ability of the enzyme to prenylate a range of compounds. The location of the bound substrates suggests a likely reaction mechanism for the conversion of (S)-benzodiazepinedione. Structure-guided mutagenesis experiments confirm that, in addition to (S)-benzodiazepinedione, CdpNPT can also act on (R)-benzodiazepinedione and several cyclic dipeptides, albeit with relaxed specificity. Finally, nuclear magnetic resonance spectroscopy demonstrates that CdpNPT is a C-3 reverse PT that catalyzes the formation of C-3β prenylated indolines from diketopiperazines of tryptophan-containing cyclic dipeptides.


  • Organizational Affiliation

    Interfakultäres Institut für Biochemie, Universität Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclic dipeptide N-prenyltransferase
A, B
428Aspergillus 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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0MV
Query on 0MV

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
(3S)-3-(1H-indol-3-ylmethyl)-3,4-dihydro-1H-1,4-benzodiazepine-2,5-dione
C18 H15 N3 O2
AQDZAHJUWYRHGM-INIZCTEOSA-N
PIS
Query on PIS

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]
TRIHYDROGEN THIODIPHOSPHATE
H3 O6 P2 S
HWTUHTNZLQJJEV-UHFFFAOYSA-M
IMD
Query on IMD

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A],
H [auth A],
K [auth B],
M [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.229 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.73α = 90
b = 137.73β = 90
c = 170.51γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 0MVClick on this verticalbar to view detailsBest fitted PISClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2012-08-29
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description