ISDA: 7NHE

Deposition Date 2021-02-10

Release Date 2021-12-22

Last Version Date 2024-10-16

Entry Detail

PDB ID:

7NHE

Keywords:

LYASE

Title:

Crystal structure of Arabidopsis thaliana Pdx1K166R-I333 complex

Biological Source:

Source Organism:

Arabidopsis thaliana (Taxon ID: 3702)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.23 Å

R-Value Free:

0.21

R-Value Work:

0.17

R-Value Observed:

0.17

Space Group:

H 3

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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

KPR

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.

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Primary Citation of related structures

Abstact

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