5MOG | pdb_00005mog

Oryza sativa phytoene desaturase inhibited by norflurazon

PDB DOI: https://doi.org/10.2210/pdb5MOG/pdb

Classification: OXIDOREDUCTASE
Organism(s): Oryza sativa Indica Group
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-12-14 Released: 2017-07-12
Deposition Author(s): Brausemann, A., Gemmecker, S., Koschmieder, J., Beyer, P., Einsle, O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.77 Å
R-Value Free:
0.224 (Depositor), 0.237 (DCC)
R-Value Work:
0.209 (Depositor), 0.217 (DCC)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of Phytoene Desaturase Provides Insights into Herbicide Binding and Reaction Mechanisms Involved in Carotene Desaturation.

Brausemann, A., Gemmecker, S., Koschmieder, J., Ghisla, S., Beyer, P., Einsle, O.

(2017) Structure 25: 1222-1232.e3

PubMed: 28669634 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2017.06.002
Primary Citation Related Structures:
5MOG

PubMed Abstract:
Cyanobacteria and plants synthesize carotenoids via a poly-cis pathway starting with phytoene, a membrane-bound C40 hydrocarbon. Phytoene desaturase (PDS) introduces two double bonds and concomitantly isomerizes two neighboring double bonds from trans to cis. PDS assembles into homo-tetramers that interact monotopically with membranes. A long hydrophobic tunnel is proposed to function in the sequential binding of phytoene and the electron acceptor plastoquinone. The herbicidal inhibitor norflurazon binds at a plastoquinone site thereby blocking reoxidation of FAD _red. Comparison with the sequence-dissimilar bacterial carotene desaturase CRTI reveals substantial similarities in the overall protein fold, defining both as members of the GR2 family of flavoproteins. However, the PDS active center architecture is unprecedented: no functional groups are found in the immediate flavin vicinity that might participate in dehydrogenation and isomerization. This suggests that the isoalloxazine moiety is sufficient for catalysis. Despite mechanistic differences, an ancient evolutionary relation of PDS and CRTI is apparent.

Organizational Affiliation

Institute for Biochemistry, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany.

Macromolecule Content

Total Structure Weight: 287.57 kDa
Atom Count: 19,520
Modeled Residue Count: 2,345
Deposited Residue Count: 2,485
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phytoene dehydrogenase, chloroplastic/chromoplastic	A, B, C, D, E	497	Oryza sativa Indica Group	Mutation(s): 0 Gene Names: PDS1, PDS, OsI_010044 EC: 1.3.99 (PDB Primary Data), 1.3.5.5 (UniProt)
UniProt
Find proteins for A2XDA1 (Oryza sativa subsp. indica) Explore A2XDA1 Go to UniProtKB: A2XDA1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A2XDA1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain T [auth D] SDF format, chain R [auth C] SDF format, chain K [auth B] SDF format, chain F [auth A] MOL2 format, chain Z [auth E] MOL2 format, chain T [auth D] MOL2 format, chain R [auth C] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] mmCIF format, chain Z [auth E] mmCIF format, chain T [auth D] mmCIF format, chain R [auth C] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A]	F [auth A], K [auth B], R [auth C], T [auth D], Z [auth E]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain Z [auth E] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain Z [auth E]
NRF Query on NRF Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain S [auth C] SDF format, chain L [auth B] SDF format, chain G [auth A] SDF format, chain AA [auth E] MOL2 format, chain U [auth D] MOL2 format, chain S [auth C] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain AA [auth E] mmCIF format, chain U [auth D] mmCIF format, chain S [auth C] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain AA [auth E]	AA [auth E], G [auth A], L [auth B], S [auth C], U [auth D]	Norflurazon C₁₂ H₉ Cl F₃ N₃ O NVGOPFQZYCNLDU-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain G [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain U [auth D] Interactions & Density Focus chain AA [auth E] Focus chain G [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain U [auth D]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain BA [auth E] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain BA [auth E] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain BA [auth E]	BA [auth E], H [auth A], I [auth A], M [auth B], N [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain BA [auth E] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain O [auth B] MOL2 format, chain V [auth D] MOL2 format, chain O [auth B] mmCIF format, chain V [auth D] mmCIF format, chain O [auth B]	O [auth B], V [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain O [auth B] Focus chain V [auth D] Interactions & Density Focus chain O [auth B] Focus chain V [auth D]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain J [auth A] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain J [auth A] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain J [auth A]	J [auth A] P [auth B] Q [auth B] W [auth D] X [auth D] J [auth A], P [auth B], Q [auth B], W [auth D], X [auth D], Y [auth D]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain J [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain J [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]