4E0U

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.jmb.2012.05.033
  • Primary Citation of Related Structures:  

  • 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 dipe ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclic dipeptide N-prenyltransferase
A, B
428Neosartorya fumigataMutation(s): 0 
Gene Names: cdpNPT
Find proteins for D1D8L6 (Neosartorya fumigata)
Go to UniProtKB:  D1D8L6
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0MV
Query on 0MV

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A, B
(3S)-3-(1H-indol-3-ylmethyl)-3,4-dihydro-1H-1,4-benzodiazepine-2,5-dione
C18 H15 N3 O2
AQDZAHJUWYRHGM-INIZCTEOSA-N
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
PIS
Query on PIS

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A, B
TRIHYDROGEN THIODIPHOSPHATE
THIOPYROPHOSPHATE
H3 O6 P2 S
HWTUHTNZLQJJEV-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

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A, B
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.196 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 137.730α = 90.00
b = 137.730β = 90.00
c = 170.510γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2012-08-29
    Type: Database references