PDBsum entry 1e2d

Phosphotransferase

PDB id: 1e2d

Contents

Protein chain

209 a.a. *

Ligands

TMP

ADP

Metals

_MG ×3

Waters ×291

* Residue conservation analysis

PDB id:

1e2d

Name:

Phosphotransferase

Title:

Human thymidylate kinase complexed with thymidine monophosphate, adenosine diphosphate and a magnesium-ion

Structure:

Thymidylate kinase. Chain: a. Synonym: tmpk. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Homo-Dimer (from PDB file)

Resolution:

1.65Å R-factor: 0.201 R-free: 0.242

Authors:

N.Ostermann,I.Schlichting,R.Brundiers,M.Konrad,J.Reinstein,T.Veit, R.S.Goody,A.Lavie

Key ref:

N.Ostermann et al. (2000). Insights into the phosphoryltransfer mechanism of human thymidylate kinase gained from crystal structures of enzyme complexes along the reaction coordinate. Structure, 8, 629-642. PubMed id: 10873853 DOI: 10.1016/S0969-2126(00)00149-0

Date:

22-May-00 Release date: 17-May-01

Protein chain

P23919  (KTHY_HUMAN) -  Thymidylate kinase from Homo sapiens

Seq: 212 a.a.

Struc: 209 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.7.4.9 - dTMP kinase.
• Reaction: dTMP + ATP = dTDP + ADP

dTMP + ATP (Bound ligand (Het Group name = TMP) corresponds exactly) = dTDP (Bound ligand (Het Group name = ADP) corresponds exactly) + ADP

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

reference

DOI no: 10.1016/S0969-2126(00)00149-0

Structure 8:629-642 (2000)

PubMed id: 10873853

Insights into the phosphoryltransfer mechanism of human thymidylate kinase gained from crystal structures of enzyme complexes along the reaction coordinate.

N.Ostermann, I.Schlichting, R.Brundiers, M.Konrad, J.Reinstein, T.Veit, R.S.Goody, A.Lavie.

ABSTRACT

BACKGROUND: Thymidylate kinase (TMPK) is a nucleoside monophosphate kinase that catalyzes the reversible phosphoryltransfer between ATP and TMP to yield ADP and TDP. In addition to its vital role in supplying precursors for DNA synthesis, human TMPK has an important medical role participating in the activation of a number of anti-HIV prodrugs. RESULTS: Crystal structures of human TMPK in complex with TMP and ADP, TMP and the ATP analog AppNHp, TMP with ADP and the phosphoryl analog AlF(3), TDP and ADP, and the bisubstrate analog TP(5)A were determined. The conformations of the P-loop, the LID region, and the adenine-binding loop vary according to the nature of the complex. Substitution of ADP by AppNHp results in partial closure of the P-loop and the rotation of the TMP phosphate group to a catalytically unfavorable position, which rotates back in the AlF(3) complex to a position suitable for in-line attack. In the fully closed state observed in the TP(5)A and the TDP-ADP complexes, Asp15 interacts strongly with the 3'-hydroxyl group of TMP. CONCLUSIONS: The observed changes of nucleotide state and conformation and the corresponding protein structural changes are correlated with intermediates occurring along the reaction coordinate and show the sequence of events occurring during phosphate transfer. The low catalytic activity of human TMPK appears to be determined by structural changes required to achieve catalytic competence and it is suggested that a mechanism might exist to accelerate the activity.

Selected figure(s)

Figure 4.
Figure 4. Conformational changes of Arg97 and the phosphoryl groups of TDP to the stable product conformation in the TDP-ADP bound complex. Overlay of the TMP/TDP-binding site of the structures of TMPK in complex with TMP, ADP and AlF[3] (red) and TDP and ADP (yellow). In the complex with bound TDP and ADP the sidechain of Arg97 rotates (90°) around the bond between the atoms CG and CD such that it cannot act as a clamp to bring both nucleotides together for the backward reaction. The figures were generated using the programs Molscript [28] and Raster 3D [29].

The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 629-642) copyright 2000.

Figure was selected by an automated process.