ISDA: 7NHF

Deposition Date 2021-02-10

Release Date 2021-12-22

Last Version Date 2024-01-31

Entry Detail

PDB ID:

7NHF

Keywords:

LYASE

Title:

Crystal structure of Arabidopsis thaliana Pdx1K166R

Biological Source:

Source Organism(s):

Arabidopsis thaliana (Taxon ID: 3702)

Expression System(s):

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.35 Å

R-Value Free:

0.24

R-Value Work:

0.21

R-Value Observed:

0.22

Space Group:

H 3

Download Validation Report

Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Pyridoxal 5'-phosphate synthase subunit PDX1.3
Gene (Uniprot):PDX13
Mutagens:K166R
Chain IDs:A, B, C, D
Chain Length:291
Number of Molecules:4
Biological Source:Arabidopsis thaliana

UniProt ID:Q8L940 Pfam ID:PF01680

Ligand Molecules

PO4

Primary Citation

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.Show

Rsc Chem Biol 3 227 230 (2022)

PMID: 35360887 DOI: 10.1039/d1cb00160d

Abstact

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 I333 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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures

Abstact

Feedback Form