7NHE

Crystal structure of Arabidopsis thaliana Pdx1K166R-I333 complex

PDB DOI: https://doi.org/10.2210/pdb7NHE/pdb

Classification: LYASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-02-10 Released: 2021-12-22
Deposition Author(s): Rodrigues, M.J., Zhang, Y., Bolton, R., Evans, G., Giri, N., Royant, A., Begley, T., Ealick, S.E., Tews, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free: 0.219
R-Value Work: 0.175
R-Value Observed: 0.177

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Trapping and structural characterisation of a covalent intermediate in vitamin B 6 biosynthesis catalysed by the Pdx1 PLP synthase.

Rodrigues, M.J., Giri, N., Royant, A., Zhang, Y., Bolton, R., Evans, G., Ealick, S.E., Begley, T., Tews, I.

(2022) RSC Chem Biol 3: 227-230

PubMed: 35360887 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1039/d1cb00160d
Primary Citation of Related Structures:
7NHE, 7NHF

PubMed Abstract:
The Pdx1 enzyme catalyses condensation of two carbohydrates and ammonia to form pyridoxal 5-phosphate (PLP) via an imine relay mechanism of carbonyl intermediates. The I ₃₃₃ intermediate characterised here using structural, UV-vis absorption spectroscopy and mass spectrometry analyses rationalises stereoselective deprotonation and subsequent substrate assisted phosphate elimination, central to PLP biosynthesis.

Organizational Affiliation

Biological Sciences, Institute for Life Sciences, University of Southampton Southampton SO17 1BJ UK ivo.tews@soton.ac.uk.

Macromolecule Content

Total Structure Weight: 126 kDa
Atom Count: 8,681
Modelled Residue Count: 1,084
Deposited Residue Count: 1,164
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxal 5'-phosphate synthase subunit PDX1.3	A, B, C, D	291	Arabidopsis thaliana	Mutation(s): 1 Gene Names: PDX13, GIP2, PDX1L3, RSR4, At5g01410, T10O8.120 EC: 4.3.3.6
UniProt
Find proteins for Q8L940 (Arabidopsis thaliana) Explore Q8L940 Go to UniProtKB: Q8L940
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8L940
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KPR (Subject of Investigation/LOI) Query on KPR Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	[(~{E},4~{S})-4-azanyl-3-oxidanylidene-pent-1-enyl] dihydrogen phosphate C₅ H₁₀ N O₅ P RTVKPJRIOVZREZ-ZPYNKGFJSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]