2EGH | pdb_00002egh

Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase complexed with a magnesium ion, NADPH and fosmidomycin

PDB DOI: https://doi.org/10.2210/pdb2EGH/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli str. K-12 substr. W3110
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-03-01 Released: 2007-06-19
Deposition Author(s): Yajima, S., Hara, K., Iino, D., Sasaki, Y., Kuzuyama, T., Seto, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.225 (Depositor), 0.217 (DCC)
R-Value Work:
0.218 (Depositor), 0.214 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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Literature

Structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase in a quaternary complex with a magnesium ion, NADPH and the antimalarial drug fosmidomycin

Yajima, S., Hara, K., Iino, D., Sasaki, Y., Kuzuyama, T., Ohsawa, K., Seto, H.

(2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 466-470

PubMed: 17554164 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309107024475
Primary Citation Related Structures:
2EGH

PubMed Abstract:
The crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) from Escherichia coli complexed with Mg(2+), NADPH and fosmidomycin was solved at 2.2 A resolution. DXR is the key enzyme in the 2-C-methyl-D-erythritol 4-phosphate pathway and is an effective target of antimalarial drugs such as fosmidomycin. In the crystal structure, electron density for the flexible loop covering the active site was clearly observed, indicating the well ordered conformation of DXR upon substrate binding. On the other hand, no electron density was observed for the nicotinamide-ribose portion of NADPH and the position of Asp149 anchoring Mg(2+) was shifted by NADPH in the active site.

Organizational Affiliation

Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan. yshun@nodai.ac.jp

Macromolecule Content

Total Structure Weight: 94.25 kDa
Atom Count: 6,482
Modeled Residue Count: 798
Deposited Residue Count: 848
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1-deoxy-D-xylulose 5-phosphate reductoisomerase	A, B	424	Escherichia coli str. K-12 substr. W3110	Mutation(s): 0 Gene Names: dxr EC: 1.1.1.267
UniProt
Find proteins for P45568 (Escherichia coli (strain K12)) Explore P45568 Go to UniProtKB: P45568
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P45568
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
FOM Query on FOM Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID C₄ H₁₀ N O₅ P GJXWDTUCERCKIX-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
FOM	BindingDB: 2EGH	IC50: min: 20, max: 438 (nM) from 6 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.225 (Depositor), 0.217 (DCC)
R-Value Work: 0.218 (Depositor), 0.214 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.59	α = 90
b = 59.115	β = 90
c = 87.05	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-06-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-06-19
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description