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

References listed in PDB file

Key reference

Title

Conformational changes in the reaction of pyridoxal kinase.

Authors

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

Ref.

J Biol Chem, 2004, 279, 17459-17465. [DOI no: 10.1074/jbc.M312380200]

PubMed id

14722069

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.

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.

Secondary reference #1

Title

Crystal structure of brain pyridoxal kinase, A novel member of the ribokinase superfamily.

Authors

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

Ref.

J Biol Chem, 2002, 277, 46385-46390. [DOI no: 10.1074/jbc.M208600200]

PubMed id

12235162

Figure 3.
Fig. 3. Substrate-binding sites of pyridoxal kinase. a, stereoview of the interactions between ATP and residues of enzyme in the complex. The bound ATP molecule is shown as a ball-and-stick model; Zn2+ and K+ are shown as spheres. b, the pyridoxal-binding site is shown as a transparent electrostatic surface. Positive regions are blue, and negative regions are red; the modeled pyridoxal and related residues are shown as sticks. The positions of the pyridine ring of pyridoxal are labeled.

Figure 5.
Fig. 5. a and b, omit electron density maps of the ATP molecules bound in the complex in monomer A (a) and monomer B (b). c, a superimposed view of the active site of pyridoxal kinase (red), ribokinase (blue), and adenosine kinase (green). The superimposition is based on the common catalytic residue Asp and the helix to which it belongs.

The above figures are reproduced from the cited reference with permission from the ASBMB

Secondary reference #2

Title

Crystallization and preliminary crystallographic studies of pyridoxal kinase from sheep brain.

Authors

M.H.Li, F.Kwok, X.M.An, W.R.Chang, C.K.Lau, J.P.Zhang, S.Q.Liu, Y.C.Leung, T.Jiang, D.C.Liang.

Ref.

Acta Crystallogr D Biol Crystallogr, 2002, 58, 1479-1481. [DOI no: 10.1107/S0907444902011034]

PubMed id

12198308

Figure 1.
Figure 1 (a) Typical trigonal crystal of pyridoxal kinase (0.12 × 0.12 × 0.5 mm); (b) typical orthorhombic crystal of pyridoxal kinase (0.15 × 0.15 × 0.4 mm).

The above figure is reproduced from the cited reference with permission from the IUCr