PDBsum entry 1rfu

Transferase

PDB id: 1rfu

Contents

Protein chains

(+ 2 more) 312 a.a. *

Ligands

PLP ×8

ADP ×8

Metals

_ZN ×8

Waters ×267

* Residue conservation analysis

PDB id:

1rfu

Name:

Transferase

Title:

Crystal structure of pyridoxal kinase complexed with adp and plp

Structure:

Pyridoxal kinase. Chain: a, b, c, d, e, f, g, h. Synonym: pyridoxine kinase. Ec: 2.7.1.35

Source:

Ovis aries. Sheep. Organism_taxid: 9940

Biol. unit:

Dimer (from PQS)

Resolution:

2.80Å R-factor: 0.229 R-free: 0.281

Authors:

D.-C.Liang,T.Jiang,M.-H.Li

Key ref:

M.H.Li et al. (2004). Conformational changes in the reaction of pyridoxal kinase. J Biol Chem, 279, 17459-17465. PubMed id: 14722069 DOI: 10.1074/jbc.M312380200

Date:

10-Nov-03 Release date: 27-Apr-04

Protein chains

P82197  (PDXK_SHEEP) -  Pyridoxal kinase from Ovis aries

Seq: 312 a.a.

Struc: 312 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.1.35 - pyridoxal kinase.
• Reaction: pyridoxal + ATP = pyridoxal 5'-phosphate + ADP + H⁺

pyridoxal + ATP = pyridoxal 5'-phosphate (Bound ligand (Het Group name = ADP) corresponds exactly) + ADP + H(+) (Bound ligand (Het Group name = PLP) matches with 93.75% similarity)

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

reference

DOI no: 10.1074/jbc.M312380200

J Biol Chem 279:17459-17465 (2004)

PubMed id: 14722069

Conformational changes in the reaction of pyridoxal kinase.

M.H.Li, F.Kwok, W.R.Chang, S.Q.Liu, S.C.Lo, J.P.Zhang, T.Jiang, D.C.Liang.

ABSTRACT

To understand the processes involved in the catalytic mechanism of pyridoxal kinase (PLK),1 we determined the crystal structures of PLK.AMP-PCP-pyridoxamine, PLK.ADP.PLP, and PLK.ADP complexes. Comparisons of these structures have revealed that PLK exhibits different conformations during its catalytic process. After the binding of AMP-PCP (an analogue that replaced ATP) and pyridoxamine to PLK, this enzyme retains a conformation similar to that of the PLK.ATP complex. The distance between the reacting groups of the two substrates is 5.8 A apart, indicating that the position of ATP is not favorable to spontaneous transfer of its phosphate group. However, the structure of PLK.ADP.PLP complex exhibited significant changes in both the conformation of the enzyme and the location of the ligands at the active site. Therefore, it appears that after binding of both substrates, the enzyme-substrate complex requires changes in the protein structure to enable the transfer of the phosphate group from ATP to vitamin B(6). Furthermore, a conformation of the enzyme-substrate complex before the transition state of the enzymatic reaction was also hypothesized.

Selected figure(s)

Figure 2.
FIG. 2. Pyridoxal binding site. The molecule in the center is the pyridoxamine bound in the PLK·AMP-PCP-pyridoxamine complex. The surrounding residues are shown in green, and the hydrogen bonds between the pyridoxamine and the residues are shown as purple dashes. The corresponding residues in the PLK·ATP complex are in blue. A comparison of these structures reveals local conformational adjustments of the pyridoxal binding site when the substrates binds.

Figure 5.
FIG. 5. The ADP molecule bound in the PLK·ADP complex and the residues interacting with it. The hydrogen bonds between them are shown as blue dashes. The molecule shown as a thin black line is the ADP in the PLK·ADP·PLP complex. A significant conformational change happens between the two ADP molecules.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 17459-17465) copyright 2004.

Figures were selected by the author.