1QXO

Crystal structure of Chorismate synthase complexed with oxidized FMN and EPSP

PDB DOI: https://doi.org/10.2210/pdb1QXO/pdb

Classification: LYASE
Organism(s): Streptococcus pneumoniae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2003-09-08 Released: 2003-12-23
Deposition Author(s): Maclean, J., Ali, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.222
R-Value Work: 0.157
R-Value Observed: 0.160

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

The structure of chorismate synthase reveals a novel flavin binding site fundamental to a unique chemical reaction

Maclean, J., Ali, S.

(2003) Structure 11: 1499-1511

PubMed: 14656434 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2003.11.005
Primary Citation of Related Structures:
1QXO

PubMed Abstract:
The crystal structure of chorismate synthase (CS) from Streptococcus pneumoniae has been solved to 2.0 A resolution in the presence of flavin mononucleotide (FMN) and the substrate 5-enolpyruvyl-3-shikimate phosphate (EPSP). CS catalyses the final step of the shikimate pathway and is a potential therapeutic target for the rational design of novel antibacterials, antifungals, antiprotozoals, and herbicides. CS is a tetramer with the monomer possessing a novel beta-alpha-beta fold. The interactions between the enzyme, cofactor, and substrate reveal the structural reasons underlying the unique catalytic mechanism and identify the amino acids involved. This structure provides the essential initial information necessary for the generation of novel anti-infective compounds by a structure-guided medicinal chemistry approach.

Organizational Affiliation

Department of Structural Biology, West of Scotland Science Park, Glasgow G20 0XP, Scotland, United Kingdom. [email protected]

Macromolecule Content

Total Structure Weight: 179.9 kDa
Atom Count: 14,427
Modelled Residue Count: 1,552
Deposited Residue Count: 1,552
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chorismate synthase	A, B, C, D	388	Streptococcus pneumoniae	Mutation(s): 12 Gene Names: AROC, SP1374 OR SPR1232 EC: 4.2.3.5
UniProt
Find proteins for P0A2Y6 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore P0A2Y6 Go to UniProtKB: P0A2Y6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A2Y6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C]	BA [auth D] CA [auth D] K [auth A] P [auth B] U [auth C] BA [auth D], CA [auth D], K [auth A], P [auth B], U [auth C], V [auth C]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain K [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain K [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C]
EPS Query on EPS Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain L [auth A] SDF format, chain Q [auth B] SDF format, chain W [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain W [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain W [auth C]	DA [auth D], L [auth A], Q [auth B], W [auth C]	5-[(1-CARBOXYVINYL)OXY]-4-HYDROXY-3-(PHOSPHONOOXY)CYCLOHEX-1-ENE-1-CARBOXYLIC ACID C₁₀ H₁₃ O₁₀ P QUTYKIXIUDQOLK-PRJMDXOYSA-N		Interactions Focus chain DA [auth D] Focus chain L [auth A] Focus chain Q [auth B] Focus chain W [auth C] Interactions & Density Focus chain DA [auth D] Focus chain L [auth A] Focus chain Q [auth B] Focus chain W [auth C]
NCO Query on NCO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D]	E [auth A] F [auth A] G [auth A] M [auth B] N [auth B] E [auth A], F [auth A], G [auth A], M [auth B], N [auth B], R [auth C], S [auth C], X [auth D], Y [auth D]	COBALT HEXAMMINE(III) Co H₁₈ N₆ DYLMFCCYOUSRTK-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain X [auth D] Focus chain Y [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain T [auth C] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain T [auth C] mmCIF format, chain Z [auth D]	AA [auth D] H [auth A] I [auth A] J [auth A] O [auth B] AA [auth D], H [auth A], I [auth A], J [auth A], O [auth B], T [auth C], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain T [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain T [auth C] Focus chain Z [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Binding Affinity Annotations
ID	Source	Binding Affinity
FMN	BindingDB: 1QXO	Kd: 2.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.222
R-Value Work: 0.157
R-Value Observed: 0.160
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.059	α = 90
b = 124.582	β = 115.15
c = 85.163	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SnB	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2003-12-23

Deposition Author(s):

Maclean, J.

Ali, S.

Revision History (Full details and data files)

Version 1.0: 2003-12-23
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary