1G0N

STRUCTURE OF TRIHYDROXYNAPHTHALENE REDUCTASE IN COMPLEX WITH NADPH AND 4,5,6,7-TETRACHLORO-PHTHALIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structures of trihydroxynaphthalene reductase-fungicide complexes: implications for structure-based design and catalysis.

Liao, D.Basarab, G.S.Gatenby, A.A.Valent, B.Jordan, D.B.

(2001) Structure 9: 19-28

  • DOI: https://doi.org/10.1016/s0969-2126(00)00548-7
  • Primary Citation of Related Structures:  
    1DOH, 1G0N, 1G0O

  • PubMed Abstract: 

    Trihydroxynaphthalene reductase catalyzes two intermediate steps in the fungal melanin biosynthetic pathway. The enzyme, a typical short-chain dehydrogenase, is the biochemical target of three commercial fungicides. The fungicides bind preferentially to the NADPH form of the enzyme. Three X-ray structures of the Magnaporthe grisea enzyme complexed with NADPH and two commercial and one experimental fungicide were determined at 1.7 A (pyroquilon), 2.0 A (2,3-dihydro-4-nitro-1H-inden-1-one, 1), and 2.1 A (phthalide) resolutions. The chemically distinct inhibitors occupy similar space within the enzyme's active site. The three inhibitors share hydrogen bonds with the side chain hydroxyls of Ser-164 and Tyr-178 via a carbonyl oxygen (pyroquilon and 1) or via a carbonyl oxygen and a ring oxygen (phthalide). Active site residues occupy similar positions among the three structures. A buried water molecule that is hydrogen bonded to the NZ nitrogen of Lys-182 in each of the three structures likely serves to stabilize the cationic form of the residue for participation in catalysis. The pro S hydrogen of NADPH (which is transferred as a hydride to the enzyme's naphthol substrates) is directed toward the carbonyl carbon of the inhibitors that mimic an intermediate along the reaction coordinate. Modeling tetrahydroxynaphthalene and trihydroxynaphthalene in the active site shows steric and electrostatic repulsion between the extra hydroxyl oxygen of the former substrate and the sulfur atom of Met-283 (the C-terminal residue), which accounts, in part, for the 4-fold greater substrate specificity for trihydroxynaphthalene over tetrahydroxynaphthalene.


  • Organizational Affiliation

    DuPont Central Research and Development Experimental Station, Wilmington, DE 19880, USA. der-ling.liao@usa.dupont.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRIHYDROXYNAPHTHALENE REDUCTASE
A, B
283Pyricularia griseaMutation(s): 3 
EC: 1.1.1.252
UniProt
Find proteins for Q12634 (Pyricularia oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958))
Explore Q12634 
Go to UniProtKB:  Q12634
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12634
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
PHH
Query on PHH

Download Ideal Coordinates CCD File 
D [auth A]4,5,6,7-TETRACHLORO-PHTHALIDE
C8 H2 Cl4 O2
NMWKWBPNKPGATC-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.195 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.5α = 90
b = 140.5β = 90
c = 72.7γ = 120
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-06-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Data collection
  • Version 1.4: 2021-11-03
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-02-07
    Changes: Data collection