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PDBsum entry 3vtk
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References listed in PDB file
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Key reference
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Title
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The structures of thymidine kinase from herpes simplex virus type 1 in complex with substrates and a substrate analogue.
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Authors
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K.Wild,
T.Bohner,
G.Folkers,
G.E.Schulz.
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Ref.
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Protein Sci, 1997,
6,
2097-2106.
[DOI no: ]
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PubMed id
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Abstract
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Thymidine kinase from Herpes simplex virus type 1 (TK) was crystallized in an
N-terminally truncated but fully active form. The structures of TK complexed
with ADP at the ATP-site and deoxythymidine-5'-monophosphate (dTMP),
deoxythymidine (dT), or idoxuridine-5'-phosphate (5-iodo-dUMP) at the
substrate-site were refined to 2.75 A, 2.8 A, and 3.0 A resolution,
respectively. TK catalyzes the phosphorylation of dT resulting in an ester, and
the phosphorylation of dTMP giving rise to an anhydride. The presented TK
structures indicate that there are only small differences between these two
modes of action. Glu83 serves as a general base in the ester reaction. Arg163
parks at an internal aspartate during ester formation and binds the
alpha-phosphate of dTMP during anhydride formation. The bound deoxythymidine
leaves a 35 A3 cavity at position 5 of the base and two sequestered water
molecules at position 2. Cavity and water molecules reduce the substrate
specificity to such an extent that TK can phosphorylate various substrate
analogues useful in pharmaceutical applications. TK is structurally homologous
to the well-known nucleoside monophosphate kinases but contains large additional
peptide segments.
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Figure 1.
ig. 1. Stereoviewofthesymmetric TK dimerwithboundADPanddTMP.Thedomainsaredefinedaccording to theNMP-kinases
asCORE(residues 46-81,143-218.227-250.323-376, yellow, Wbi n,j (82-142, red), and ID (219-226, blue).The 72 additional
residuesaroundosition 90 are green.Mobileparts are givenasdashedlines,thetwofold axis is inserted,secondary structures are
defined in Fig. 2.
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Figure 3.
Fig. 3. Final (2F0 - F,)-electron density maps or all substrates with the C trace of the P-loop as reference. All maps are contoured
at the .0 (T level. A: ADPanddTPat 8, B: ADP and dTat 2.8 8, resolution. C: ADPand at 3.0 8,
resolution.
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The above figures are
reprinted
from an Open Access publication published by the Protein Society:
Protein Sci
(1997,
6,
2097-2106)
copyright 1997.
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Secondary reference #1
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Title
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The three-Dimensional structure of thymidine kinase from herpes simplex virus type 1.
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Authors
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K.Wild,
T.Bohner,
A.Aubry,
G.Folkers,
G.E.Schulz.
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Ref.
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FEBS Lett, 1995,
368,
289-292.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1. Sketch of the chain fold of thymidine kinase from Herpes
simplex virus type 1. To avoid crossovers the sketch is somewhat sim-
plified rendering some helix positions disputable. All ,B-strands (quad-
rangles) run towards the viewer, the orientations of the helices (circles)
are indicated by the arrows. Dashed lines denote chain segments that
are not yet modeled. The central residues of secondary structure ele-
ments bl, b2, b3, b4, b5, al, a, a3 a4, a5, a6, a7, a8, a9, al0, al 1, and
a12 are 52, 79, 159, 203, 326, 67, 87, 103, 131, 72, 190, 215, 239, 292,
314, 340, and 364, respectively.
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Figure 2.
Fig. 2. Stereo-view of the current a-backbone of dimeric thymidine kinase from Herpes simplex virus type 1 with numbering and the bound substrates
thymidine and ATP. The dashed lines indicate regions of low density which have not yet been modeled. The chosen orientation emphasizes the
planarity of the interface. The two-fold axis runs from the lefthand side in the front to the right hand side in the rear.
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The above figures are
reproduced from the cited reference
with permission from the Federation of European Biochemical Societies
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Secondary reference #2
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Title
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A fast method for obtaining highly pure recombinant herpes simplex virus type 1 thymidine kinase.
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Authors
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J.Fetzer,
M.Michael,
T.Bohner,
R.Hofbauer,
G.Folkers.
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Ref.
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Protein Expr Purif, 1994,
5,
432-441.
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PubMed id
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