PDBsum entry 2qqe

Transferase

PDB id: 2qqe

Contents

Protein chains

164 a.a. *

Ligands

THM ×2

Metals

_ZN ×2

Waters ×49

* Residue conservation analysis

PDB id:

2qqe

Name:

Transferase

Title:

Thymidine kinase from thermotoga maritima in complex with thymidine

Structure:

Thymidine kinase. Chain: a, b. Engineered: yes

Source:

Thermotoga maritima. Organism_taxid: 2336. Gene: tdk. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Resolution:

1.90Å R-factor: 0.241 R-free: 0.286

Authors:

D.Segura-Pena,J.Lichter,M.Trani,M.Konrad,A.Lavie,S.Lutz

Key ref:

D.Segura-Peña et al. (2007). Quaternary structure change as a mechanism for the regulation of thymidine kinase 1-like enzymes. Structure, 15, 1555-1566. PubMed id: 18073106 DOI: 10.1016/j.str.2007.09.025

Date:

26-Jul-07 Release date: 16-Oct-07

Protein chains

Q9WYN2  (KITH_THEMA) -  Thymidine kinase from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 184 a.a.

Struc: 164 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.1.21 - thymidine kinase.
• Reaction: thymidine + ATP = dTMP + ADP + H⁺

thymidine + ATP (Bound ligand (Het Group name = THM) corresponds exactly) = dTMP + ADP + H(+)

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

reference

DOI no: 10.1016/j.str.2007.09.025

Structure 15:1555-1566 (2007)

PubMed id: 18073106

Quaternary structure change as a mechanism for the regulation of thymidine kinase 1-like enzymes.

D.Segura-Peña, J.Lichter, M.Trani, M.Konrad, A.Lavie, S.Lutz.

ABSTRACT

The human cytosolic thymidine kinase (TK) and structurally related TKs in prokaryotes play a crucial role in the synthesis and regulation of the cellular thymidine triphosphate pool. We report the crystal structures of the TK homotetramer from Thermotoga maritima in four different states: its apo-form, a binary complex with thymidine, as well as the ternary structures with the two substrates (thymidine/AppNHp) and the reaction products (TMP/ADP). In combination with fluorescence spectroscopy and mutagenesis experiments, our results demonstrate that ATP binding is linked to a substantial reorganization of the enzyme quaternary structure, leading to a transition from a closed, inactive conformation to an open, catalytic state. We hypothesize that these structural changes are relevant to enzyme function in situ as part of the catalytic cycle and serve an important role in regulating enzyme activity by amplifying the effects of feedback inhibitor binding.

Selected figure(s)

Figure 1.
Figure 1. The TmTK Three-Dimensional Structure Remains Largely Unchanged upon Substrate Binding
(A) Stereo view of an overlay of three TmTK backbones in different complexation states. Apo-form in cyan, in complex with thymidine in yellow and the ternary complex in magenta. Purple spheres represent the Mg ion in the active site.
(B) Ribbon representation of the three individual TmTK structures, using the same color code as in (A). Yellow spheres mark the position of the structural zinc atom. The two regions of the protein that undergo a conformational change upon substrate binding are the lasso loop (red lines) and the β-hairpin loop (blue lines). The dashed lines represent parts of the flexible loops that could not be modeled due to lack of electron density. Most of the lasso loop, which is involved in thymidine binding, was disorganized in the apo-form, yet became almost fully defined in the complex with thymidine, and could be completely modeled in the ground-state complex (thymidine + AppNHp). The β-hairpin loop composed of βc1/β3 is sensitive to the presence of phosphoryl donor. Only in the presence of AppNHp was the electron density for βc1 present.

Figure 3.
Figure 3. ATP Induces a Quaternary Structural Rearrangement in TmTK
(A) Sphere representation of TmTK homotetramer in the three substrate-binding states. Individual monomers are shown in different colors. Note that, upon ATP binding, the tetramer expands due to an increase in the separation between the monomers that make the interface to which the adenosine moiety of ATP is bound (weak dimer interface, horizontal brackets). In contrast the second type of monomer-monomer interface remains unchanged (vertical brackets). ATP and thymidine are shown in yellow and green, respectively.
(B) Stereo view overlay of the TmTK apo-tetramer (cyan) with the tetramer in complex with thymidine (yellow). The overlay was done on the monomer A (Ma). There is an excellent superposition of the two tetrameric structures, indicating the same subunit organization for the two tetrameric structures.
(C) Analogous stereoview overlay between the TmTK binary complex (with thymidine) and the ternary complex (magenta color). Subunits across the strong dimer interface show an excellent overlay (Ma and Mb). In constrast, the relative orientation of the remaining two monomers is changed. Note the change of orientation between monomers across the weak interface (Md with respect to Ma and Mc with respect to Mb). Black lines mark the positions of helix α1 in each tetramer. In the closed state of the tetramer (binary complex in yellow), helix α1 would clash with the adenosine moiety of ATP.

The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2007, 15, 1555-1566) copyright 2007.

Figures were selected by the author.