PDBsum entry 5k3v

Biosynthetic protein

PDB id: 5k3v

Contents

Protein chains

276 a.a.

Ligands

SO4 ×8

EDO ×3

Metals

_CL ×5

Waters ×501

PDB id:

5k3v

Name:

Biosynthetic protein

Title:

Apo-pdx1.3 (arabidopsis)

Structure:

Pyridoxal 5'-phosphate synthase subunit pdx1.3. Chain: a, b, c, d. Synonym: plp synthase subunit pdx1.3. Engineered: yes

Source:

Arabidopsis thaliana. Mouse-ear cress. Organism_taxid: 3702. Gene: pdx13, gip2, pdx1l3, rsr4, at5g01410, t10o8.120. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.90Å R-factor: 0.178 R-free: 0.203

Authors:

G.C.Robinson,M.Kaufmann,C.Roux,T.B.Fitzpatrick

Key ref:

G.C.Robinson et al. (2016). Structural definition of the lysine swing in Arabidopsis thaliana PDX1: Intermediate channeling facilitating vitamin B6 biosynthesis. Proc Natl Acad Sci U S A, 113, E5821. PubMed id: 27647886 DOI: 10.1073/pnas.1608125113

Date:

20-May-16 Release date: 05-Oct-16

Protein chains

Q8L940  (PDX13_ARATH) -  Pyridoxal 5'-phosphate synthase subunit PDX1.3 from Arabidopsis thaliana

Seq: 309 a.a.

Struc: 276 a.a.

Enzyme reactions

• Enzyme class: E.C.4.3.3.6 - pyridoxal 5'-phosphate synthase (glutamine hydrolyzing).
• Reaction: aldehydo-D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = pyridoxal 5'-phosphate + L-glutamate + phosphate + 3 H2O + H⁺

aldehydo-D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate (Bound ligand (Het Group name = EDO) matches with 40.00% similarity) + L-glutamine = pyridoxal 5'-phosphate + L-glutamate + phosphate + 3 × H2O + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.1608125113

Proc Natl Acad Sci U S A 113:E5821 (2016)

PubMed id: 27647886

Structural definition of the lysine swing in Arabidopsis thaliana PDX1: Intermediate channeling facilitating vitamin B6 biosynthesis.

G.C.Robinson, M.Kaufmann, C.Roux, T.B.Fitzpatrick.

ABSTRACT

No abstract given.