|
|
call loadScript javascripts\jsmol\core\package.js call loadScript javascripts\jsmol\core\core.z.js -- required by ClazzNode call loadScript javascripts\jsmol\J\awtjs2d\WebOutputChannel.js Jmol JavaScript applet jmolApplet0_object__1103706717931141__ initializing getValue debug = null getValue logLevel = null getValue allowjavascript = null AppletRegistry.checkIn(jmolApplet0_object__1103706717931141__) call loadScript javascripts\jsmol\core\corestate.z.js viewerOptions: { "name":"jmolApplet0_object","applet":true,"documentBase":"https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:10530","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0_object__1103706717931141__","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol.MyStatusListener object]","codeBase":"https://www.ebi.ac.uk/chebi/javascripts/jsmol/","syncId":"1103706717931141","bgcolor":"#000" } (C) 2012 Jmol Development Jmol Version: 13.2.7 $Date: 2013-10-01 11:35:15 -0500 (Tue, 01 Oct 2013) $ java.vendor: j2s java.version: 0.0 os.name: j2s Access: ALL memory: 0.0/0.0 processors available: 1 useCommandThread: false appletId:jmolApplet0_object (signed) starting HoverWatcher_1 getValue emulate = null defaults = "Jmol" getValue boxbgcolor = null getValue bgcolor = #000 backgroundColor = "#000" getValue ANIMFRAMECallback = null getValue APPLETREADYCallback = Jmol._readyCallback APPLETREADYCallback = "Jmol._readyCallback" getValue ATOMMOVEDCallback = null getValue CLICKCallback = null getValue ECHOCallback = null getValue ERRORCallback = null getValue EVALCallback = null getValue HOVERCallback = null getValue LOADSTRUCTCallback = null getValue MEASURECallback = null getValue MESSAGECallback = null getValue MINIMIZATIONCallback = null getValue PICKCallback = null getValue RESIZECallback = null getValue SCRIPTCallback = null getValue SYNCCallback = null getValue STRUCTUREMODIFIEDCallback = null getValue doTranslate = null language=en_US getValue popupMenu = null getValue script = null Jmol applet jmolApplet0_object__1103706717931141__ ready call loadScript javascripts\jsmol\core\corescript.z.js call loadScript javascripts\jsmol\J\script\FileLoadThread.js starting QueueThread0_2 script 1 started starting HoverWatcher_3 starting HoverWatcher_4 The Resolver thinks Mol TTP - Ideal conformer Mrv1927 07272110573D starting HoverWatcher_5 Time for openFile(TTP - Ideal conformer Mrv1927 07272110573D 46 47 0 0 0 0 999 V2000 -0.7690 0.0020 1.5360 P 0 0 1 0 0 5 0 0 0 0 0 0 0.0460 -1.2090 1.2990 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1940 -0.4220 2.1530 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0040 0.9700 2.5710 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1880 0.1350 3.9340 P 0 0 1 0 0 5 0 0 0 0 0 0 -1.1370 -0.2570 4.4630 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0590 -1.1840 3.6360 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9500 1.0480 5.0190 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1080 0.1550 6.3490 P 0 0 1 0 0 5 0 0 0 0 0 0 1.8950 -1.0580 6.0380 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8670 1.0110 7.4830 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3480 -0.2710 6.8850 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9960 0.7770 0.1440 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6750 -0.1290 -0.7270 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.9230 0.5480 -2.0760 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6740 0.8180 -2.7510 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6600 -0.4130 -3.0430 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.0740 -0.3410 -2.8540 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2580 0.1490 -4.4280 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9780 0.9600 -4.1490 C 0 0 2 0 0 0 0 0 0 0 0 0 0.1280 0.4380 -4.9550 N 0 0 0 0 0 0 0 0 0 0 0 0 0.5130 -0.8420 -4.8090 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0620 -1.5530 -4.0080 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5260 -1.3470 -5.5360 N 0 0 0 0 0 0 0 0 0 0 0 0 2.1710 -0.5730 -6.4320 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0880 -1.0300 -7.0910 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7790 0.7770 -6.5930 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4870 1.6640 -7.5840 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7600 1.2580 -5.8500 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6930 0.3930 2.2920 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9130 -0.8840 3.2930 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9400 0.4410 8.2610 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8270 0.5460 7.0760 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6290 -0.4140 -0.2830 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0630 -1.0190 -0.8740 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4920 1.4680 -1.9430 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3040 -1.4360 -2.9200 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4760 -0.8880 -3.5430 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0420 0.7960 -4.8190 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0500 -0.6630 -5.1240 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1460 2.0110 -4.3870 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7900 -2.2730 -5.4180 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2740 1.0980 -8.0820 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7730 2.0220 -8.3260 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9260 2.5140 -7.0620 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4450 2.2850 -5.9620 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 1 3 1 1 0 0 0 1 4 1 0 0 0 0 1 13 1 0 0 0 0 3 30 1 0 0 0 0 5 4 1 6 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 5 8 1 0 0 0 0 7 31 1 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 9 12 1 0 0 0 0 11 32 1 0 0 0 0 12 33 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 14 34 1 0 0 0 0 14 35 1 0 0 0 0 15 16 1 0 0 0 0 15 17 1 0 0 0 0 15 36 1 1 0 0 0 16 20 1 0 0 0 0 17 18 1 0 0 0 0 17 19 1 0 0 0 0 17 37 1 6 0 0 0 18 38 1 0 0 0 0 19 20 1 0 0 0 0 19 39 1 0 0 0 0 19 40 1 0 0 0 0 20 21 1 0 0 0 0 20 41 1 6 0 0 0 21 22 1 0 0 0 0 21 29 1 0 0 0 0 22 23 2 0 0 0 0 22 24 1 0 0 0 0 24 25 1 0 0 0 0 24 42 1 0 0 0 0 25 26 2 0 0 0 0 25 27 1 0 0 0 0 27 28 1 0 0 0 0 27 29 2 0 0 0 0 28 43 1 0 0 0 0 28 44 1 0 0 0 0 28 45 1 0 0 0 0 29 46 1 0 0 0 0 M END): 17 ms reading 46 atoms ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. Default Van der Waals type for model set to Babel 46 atoms created ModelSet: not autobonding; use forceAutobond=true to force automatic bond creation Script completed Jmol script terminated
|
| Thymidine triphosphate (TTP), also called deoxythymidine triphosphate (dTTP),
is one of the four nucleoside triphosphates that are used in the in vivo synthesis of DNA. Unlike the other deoxyribonucleoside triphosphates, thymidine triphosphate does not always contain the "deoxy" prefix in its name. This is because dTTP does not have a corresponding ribonucleoside triphosphate, as the uridine triphosphate, which lacks thymidine's 5-methylation, is used instead.
dTTP is synthesized via the methylation of dUMP via thymidylate synthase.
It can be used by DNA ligase to create overlapping "sticky ends" so that protruding ends of opened microbial plasmids may be closed up. |
|
Read full article at Wikipedia
|
InChI=1S/C10H17N2O14P3/c1- 5-3-12(10(15)11-9(5)14)8-2-6(13)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,21,22)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1 |
| NHVNXKFIZYSCEB-XLPZGREQSA-N |
| CC1=CN([C@H]2C[C@H](O)[C@@H](COP(O)(=O)OP(O)(=O)OP(O)(O)=O)O2)C(=O)NC1=O |
|
|
Mus musculus
(NCBI:txid10090)
|
Source: BioModels - MODEL1507180067
See:
PubMed
|
|
Escherichia coli
(NCBI:txid562)
|
See:
PubMed
|
|
Escherichia coli
(NCBI:txid562)
|
Found in
whole organism
(UBERON:0000468).
From MetaboLights
See:
MetaboLights Study
|
|
Escherichia coli metabolite
Any bacterial metabolite produced during a metabolic reaction in Escherichia coli.
mouse metabolite
Any mammalian metabolite produced during a metabolic reaction in a mouse (Mus musculus).
(via nucleoside 5'-triphoshate )
|
|
View more via ChEBI Ontology
|
thymidine 5'-(tetrahydrogen triphosphate)
|
|
2'-deoxythymidine 5'-triphosphate
|
ChEBI
|
|
2'-deoxythymidine triphosphate
|
ChemIDplus
|
|
5'-TTP
|
ChemIDplus
|
|
deoxy-TTP
|
ChemIDplus
|
|
deoxythymidine 5'-triphosphate
|
KEGG COMPOUND
|
|
deoxythymidine triphosphate
|
KEGG COMPOUND
|
|
dThd5'PPP
|
CBN
|
|
dTTP
|
KEGG COMPOUND
|
|
pppdT
|
CBN
|
|
thymidine 5'-triphosphate
|
ChemIDplus
|
|
THYMIDINE-5'-TRIPHOSPHATE
|
PDBeChem
|
|
TTP
|
KEGG COMPOUND
|
|
365-08-2
|
CAS Registry Number
|
ChemIDplus
|
|
71453
|
Beilstein Registry Number
|
Beilstein
|
Kapustina Ž, Jasponė A, Dubovskaja V, Mackevičius G, Lubys A (2021)
Enzymatic Synthesis of Chimeric DNA Oligonucleotides by in Vitro Transcription with dTTP, dCTP, dATP, and 2'-Fluoro Modified dGTP.
ACS synthetic biology 10, 1625-1632 [PubMed:34110794]
[show Abstract]
Efficient ways to produce single-stranded DNA are of great interest for diverse applications in molecular biology and nanotechnology. In the present study, we selected T7 RNA polymerase mutants with reduced substrate specificity to employ an in vitro transcription reaction for the synthesis of chimeric DNA oligonucleotides, either individually or in pools. We performed in vitro evolution based on fluorescence-activated droplet sorting and identified mutations V783M, V783L, V689Q, and G555L as novel variants leading to relaxed substrate discrimination. Transcribed chimeric oligonucleotides were tested in PCR, and the quality of amplification products as well as fidelity of oligonucleotide synthesis were assessed by NGS. We concluded that enzymatically produced chimeric DNA transcripts contain significantly fewer deletions and insertions compared to chemically synthesized counterparts and can successfully serve as PCR primers, making the evolved enzymes superior for simple and cheap one-pot synthesis of multiple chimeric DNA oligonucleotides in parallel using a plethora of premixed templates. | Zhou D, Lv X, Wang Y, Liu H, Luo S, Li W, Huang G (2021)
Folic acid alleviates age-related cognitive decline and inhibits apoptosis of neurocytes in senescence-accelerated mouse prone 8: deoxythymidine triphosphate biosynthesis as a potential mechanism.
The Journal of nutritional biochemistry 97, 108796 [PubMed:34102282]
[show Abstract]
Disturbed deoxythymidine triphosphate biosynthesis due to the inhibition of thymidylate synthase (TS) can lead to uracil accumulation in DNA, eventually, lead to neurocytes apoptosis and cognitive decline. Folic acid supplementation delayed cognitive decline and neurodegeneration in senescence-accelerated mouse prone 8 (SAMP8). Whether folic acid, one of nutrition factor, the effect on the expression of TS is unknown. The study aimed to determine if folic acid supplementation could alleviate age-related cognitive decline and apoptosis of neurocytes by increasing TS expression in SAMP8 mice. According to folic acid concentration in diet, four-month-old male SAMP8 mice were randomly divided into three different diet groups by baseline body weight in equal numbers. Moreover, to evaluate the role of TS, a TS inhibitor was injected intraperitoneal. Cognitive test, apoptosis rates of neurocytes, expression of TS, relative uracil level in telomere, and telomere length in brain tissue were detected. The results showed that folic acid supplementation decreased deoxyuridine monophosphate accumulation, uracil misincorporation in telomere, alleviated telomere length shorting, increased expression of TS, then decreased apoptosis rates of neurocytes, and alleviated cognitive performance in SAMP8 mice. Moreover, at the same concentration of folic acid, TS inhibitor raltitrexed increased deoxyuridine monophosphate accumulation, uracil misincorporation in telomere, and exacerbated telomere length shorting, decreased expression of TS, then increased apoptosis rates of neurocytes, and decreased cognitive performance in SAMP8 mice. In conclusion, folic acid supplementation alleviated age-related cognitive decline and inhibited apoptosis of neurocytes by increasing TS expression in SAMP8 mice. | Martínez-Arribas B, Requena CE, Pérez-Moreno G, Ruíz-Pérez LM, Vidal AE, González-Pacanowska D (2020)
DCTPP1 prevents a mutator phenotype through the modulation of dCTP, dTTP and dUTP pools.
Cellular and molecular life sciences : CMLS 77, 1645-1660 [PubMed:31377845]
[show Abstract]
To maintain dNTP pool homeostasis and preserve genetic integrity of nuclear and mitochondrial genomes, the synthesis and degradation of DNA precursors must be precisely regulated. Human all-alpha dCTP pyrophosphatase 1 (DCTPP1) is a dNTP pyrophosphatase with high affinity for dCTP and 5'-modified dCTP derivatives, but its contribution to overall nucleotide metabolism is controversial. Here, we identify a central role for DCTPP1 in the homeostasis of dCTP, dTTP and dUTP. Nucleotide pools and the dUTP/dTTP ratio are severely altered in DCTPP1-deficient cells, which exhibit an accumulation of uracil in genomic DNA, the activation of the DNA damage response and both a mitochondrial and nuclear hypermutator phenotype. Notably, DNA damage can be reverted by incubation with thymidine, dUTPase overexpression or uracil-DNA glycosylase suppression. Moreover, DCTPP1-deficient cells are highly sensitive to down-regulation of nucleoside salvage. Our data indicate that DCTPP1 is crucially involved in the provision of dCMP for thymidylate biosynthesis, introducing a new player in the regulation of pyrimidine dNTP levels and the maintenance of genomic integrity. | Yang Z, Gong C, Hu Y, Zhong J, Xia J, Xie W, Yang X, Guo Z, Wang S, Wu Q, Zhang Y (2020)
Two Deoxythymidine Triphosphate Synthesis-Related Genes Regulate Obligate Symbiont Density and Reproduction in the Whitefly Bemisia tabaci MED.
Frontiers in physiology 11, 574749 [PubMed:33716755]
[show Abstract]
Deoxythymidine triphosphate (dTTP) is essential for DNA synthesis and cellular growth in all organisms. Here, genetic capacity analysis of the pyrimidine pathway in insects and their symbionts revealed that dTTP is a kind of metabolic input in several host insect/obligate symbiont symbiosis systems, including Bemisia tabaci MED/Candidatus Portiera aleyrodidarum (hereafter Portiera). As such, the roles of dTTP on both sides of the symbiosis system were investigated in B. tabaci MED/Portiera. Dietary RNA interference (RNAi) showed that suppressing dTTP production significantly reduced the density of Portiera, significantly repressed the expression levels of horizontally transferred essential amino acid (EAA) synthesis-related genes, and significantly decreased the reproduction of B. tabaci MED adults as well as the hatchability of their offspring. Our results revealed the regulatory role of dTTP in B. tabaci MED/Portiera and showed that dTTP synthesis-related genes could be potential targets for controlling B. tabaci as well as other sucking pests. | Le Ret M, Belcher S, Graindorge S, Wallet C, Koechler S, Erhardt M, Williams-Carrier R, Barkan A, Gualberto JM (2018)
Efficient Replication of the Plastid Genome Requires an Organellar Thymidine Kinase.
Plant physiology 178, 1643-1656 [PubMed:30305373]
[show Abstract]
Thymidine kinase (TK) is a key enzyme of the salvage pathway that recycles thymidine nucleosides to produce deoxythymidine triphosphate. Here, we identified the single TK of maize (Zea mays), denoted CPTK1, as necessary in the replication of the plastidial genome (cpDNA), demonstrating the essential function of the salvage pathway during chloroplast biogenesis. CPTK1 localized to both plastids and mitochondria, and its absence resulted in an albino phenotype, reduced cpDNA copy number and a severe deficiency in plastidial ribosomes. Mitochondria were not affected, indicating they are less reliant on the salvage pathway. Arabidopsis (Arabidopsis thaliana) TKs, TK1A and TK1B, apparently resulted from a gene duplication after the divergence of monocots and dicots. Similar but less-severe effects were observed for Arabidopsis tk1a tk1b double mutants in comparison to those in maize cptk1 TK1B was important for cpDNA replication and repair in conditions of replicative stress but had little impact on the mitochondrial phenotype. In the maize cptk1 mutant, the DNA from the small single-copy region of the plastidial genome was reduced to a greater extent than other regions, suggesting preferential abortion of replication in this region. This was accompanied by the accumulation of truncated genomes that resulted, at least in part, from unfaithful microhomology-mediated repair. These and other results suggest that the loss of normal cpDNA replication elicits the mobilization of new replication origins around the rpoB (beta subunit of plastid-encoded RNA polymerase) transcription unit and imply that increased transcription at rpoB is associated with the initiation of cpDNA replication. | Gnanasekaran R (2017)
Probing the communication of deoxythymidine triphosphate in HIV-1 reverse transcriptase by communication maps and interaction energy studies.
Physical chemistry chemical physics : PCCP 19, 29608-29616 [PubMed:29083013]
[show Abstract]
We calculate communication maps for HIV-1 Reverse Transcriptase (RT) to elucidate energy transfer pathways between deoxythymidine triphosphate (dTTP) and other parts of the protein. This approach locates energy transport channels from the dTTP to remote regions of the protein via residues and water molecules. We examine the water dynamics near the catalytic site of HIV-1 RT by molecular dynamics (MD) simulations. We find that, within the catalytic site, the relaxation of water molecules is similar to that of the hydration water molecules present in other proteins and the relaxation time scale is fast enough to transport energy and helps in communication between dTTP and other residues in the system. To quantify energy transfer, we also calculate the interaction energies of dTTP, 2Mg2+, doxy-guanosine nucleotide (DG22) with their surrounding residues by using the B3LYP-D3 method. The results, from classical vibrational energy diffusivity and QM interaction energy, are complementary to identify the important residues involved in the process of polymerization. The positive and negative interactions by dTTP with different types of residues in the catalytic region make the residues transfer energy through vibrational communication. | Desler C, Frederiksen JH, Angleys M, Maynard S, Keijzers G, Fagerlund B, Mortensen EL, Osler M, Lauritzen M, Bohr VA, Rasmussen LJ (2015)
Increased deoxythymidine triphosphate levels is a feature of relative cognitive decline.
Mitochondrion 25, 34-37 [PubMed:26408413]
[show Abstract]
Mitochondrial bioenergetics, mitochondrial reactive oxygen species (ROS) and cellular levels of nucleotides have been hypothesized as early indicators of Alzheimer's disease (AD). Utilizing relative decline of cognitive ability as a predictor of AD risk, we evaluated the correlation between change of cognitive ability and mitochondrial bioenergetics, ROS and cellular levels of deoxyribonucleotides. Change of cognitive abilities, scored at ages of approximately 20 and 57 was determined for a cohort of 1985 male participants. Mitochondrial bioenergetics, mitochondrial ROS and whole-cell levels of deoxyribonucleotide triphosphates were measured in peripheral blood mononuclear cells (PBMCs) from a total of 103 selected participants displaying the most pronounced relative cognitive decline and relative cognitive improvement. We show that relative cognitive decline is associated with higher PBMC content of deoxythymidine-triphosphate (dTTP) (20%), but not mitochondrial bioenergetics parameters measured in this study or mitochondrial ROS. Levels of dTTP in PBMCs are indicators of relative cognitive change suggesting a role of deoxyribonucleotides in the etiology of AD. | Wang N, Jiang J, Li X, Tan H, Zheng J, Chen G, Jia Z (2015)
Molecular Dynamics Simulation Studies of dTTP Binding and Catalysis Mediated by YhdE Dimerization.
PloS one 10, e0134879 [PubMed:26252214]
[show Abstract]
YhdE is a Maf-like (multicopy associated filamentation) protein that primarily acts as dTTPase to hydrolyze dTTP into dTMP and two phosphate molecules in cell metabolism pathway. Two crystal structures of YhdE have been previously determined, representing the open and closed active site conformations, respectively. Based on the structures, we have carried out molecular dynamics simulations and free energy calculations to investigate dTTP binding to and hydrolysis by YhdE. Our results suggest that YhdE closed state is structurally more compact than its open state at room temperature. YhdE open state is a favorable conformation for dTTP binding and closed state is a structurally favorable conformation for catalytic reaction. This observation is supported by the structure of YhdE homolog in complex with a nucleotide analog. Free energy calculations reveal that YhdE dimerization occurs preferentially in dTTP binding and is favorable for successive cooperative reaction. The key residues R11, R12 and K80, are found to contribute to the substrate stabilization. Further, YhdE dimerization and binding of dTTP induce the cooperative effect through a direct allosteric communication network in YhdE from the dTTP binding sites in the catalytic center to the intermolecular β-strand in YhdE dimer. | Helt SS, Thymark M, Harris P, Aagaard C, Dietrich J, Larsen S, Willemoes M (2008)
Mechanism of dTTP inhibition of the bifunctional dCTP deaminase:dUTPase encoded by Mycobacterium tuberculosis.
Journal of molecular biology 376, 554-569 [PubMed:18164314]
[show Abstract]
Recombinant deoxycytidine triphosphate (dCTP) deaminase from Mycobacterium tuberculosis was produced in Escherichia coli and purified. The enzyme proved to be a bifunctional dCTP deaminase:deoxyuridine triphosphatase. As such, the M. tuberculosis enzyme is the second bifunctional enzyme to be characterised and provides evidence for bifunctionality of dCTP deaminase occurring outside the Archaea kingdom. A steady-state kinetic analysis revealed that the affinity for dCTP and deoxyuridine triphosphate as substrates for the synthesis of deoxyuridine monophosphate were very similar, a result that contrasts that obtained previously for the archaean Methanocaldococcus jannaschii enzyme, which showed approximately 10-fold lower affinity for deoxyuridine triphosphate than for dCTP. The crystal structures of the enzyme in complex with the inhibitor, thymidine triphosphate, and the apo form have been solved. Comparison of the two shows that upon binding of thymidine triphosphate, the disordered C-terminal arranges as a lid covering the active site, and the enzyme adapts an inactive conformation as a result of structural changes in the active site. In the inactive conformation dephosphorylation cannot take place due to the absence of a water molecule otherwise hydrogen-bonded to O2 of the alpha-phosphate. | El Omari K, Solaroli N, Karlsson A, Balzarini J, Stammers DK (2006)
Structure of vaccinia virus thymidine kinase in complex with dTTP: insights for drug design.
BMC structural biology 6, 22 [PubMed:17062140]
[show Abstract]
BackgroundDevelopment of countermeasures to bioterrorist threats such as those posed by the smallpox virus (variola), include vaccination and drug development. Selective activation of nucleoside analogues by virus-encoded thymidine (dThd) kinases (TK) represents one of the most successful strategies for antiviral chemotherapy as demonstrated for anti-herpes drugs. Vaccinia virus TK is a close orthologue of variola TK but also shares a relatively high sequence identity to human type 2 TK (hTK), thus achieving drug selectivity relative to the host enzyme is challenging.ResultsIn order to identify any differences compared to hTK that may be exploitable in drug design, we have determined the crystal structure of VVTK, in complex with thymidine 5'-triphosphate (dTTP). Although most of the active site residues are conserved between hTK and VVTK, we observe a difference in conformation of residues Asp-43 and Arg-45. The equivalent residues in hTK hydrogen bond to dTTP, whereas in subunit D of VVTK, Asp-43 and Arg-45 adopt a different conformation preventing interaction with this nucleotide. Asp-43 and Arg-45 are present in a flexible loop, which is disordered in subunits A, B and C. The observed difference in conformation and flexibility may also explain the ability of VVTK to phosphorylate (South)-methanocarbathymine whereas, in contrast, no substrate activity with hTK is reported for this compound.ConclusionThe difference in conformation for Asp-43 and Arg-45 could thus be used in drug design to generate VVTK/Variola TK-selective nucleoside analogue substrates and/or inhibitors that have lower affinity for hTK. | Ma XD, Ke T, Li YX, Huang CX, Song AD, Chen HG, Wu YH, Jia XC, He GY (2004)
In vitro mutagenesis of Xanthomonas campestris α-amylase gene by partially replacing deoxythymidine triphosphate with 5-bromo-2'-deoxyuridine-5'-triphosphate using a PCR technique
Biotechnology letters 26, 171-175 [Agricola:IND43614414]
[show Abstract]
Three mutants of the wild type α-amylase gene from Xanthomonas campestris pv. campestris 8004 were obtained using a PCR technique in which deoxythymidine triphosphate (dTTP) was partially replaced by 5-bromo-2'-deoxyuridine-5'-triphosphate (BrdUTP), at an optimal dTTP:BrdUTP ratio of 1000:1. Of the three mutants that were obtained and which were sequenced, one mutant with 40 times higher activity than the wild type α-amylase gene product was obtained by using primary PCR products as a template for a second PCR reaction. | He Q, Skog S, Welander I, Tribukait B (2002)
X-irradiation effects on thymidine kinase (TK): II. The significance of deoxythymidine triphosphate for inhibition of TK1 activity.
Cell proliferation 35, 83-92 [PubMed:11952643]
[show Abstract]
The purpose of this study was to investigate the mechanism behind the high sensitivity of thymidine kinase 1 (TK1) to X-irradiation. The deoxythymidine triphosphate (dTTP) pool was studied in mouse ascites tumour cells 1-24 h after X-irradiation with 5 Gy. Irradiation changed the Michaelis-Menten kinetics of TK1 from linear to biphasic, showing a negative co-operativity. These changes were closely related to changes in the dTTP pool. Addition of dTTP to the cell extract of non-irradiated cells, or thymidine (dTdR) to the culture medium, resulted in changes very similar to the kinetics found in the irradiated cells. Addition of 5 cent-amino-5 cent-deoxythymidine (5 cent-AdTdR), a thymidine analogue that eliminated the inhibitory effect of dTTP on TK1 activity, completely abolished the irradiation-induced inhibition of TK1 activity. We suggest that the reduced TK1 activity is mainly due to an elevated intracellular concentration of dTTP. | Roberts JD, Izuta S, Thomas DC, Kunkel TA (1994)
Mispair-, site-, and strand-specific error rates during simian virus 40 origin-dependent replication in vitro with excess deoxythymidine triphosphate.
The Journal of biological chemistry 269, 1711-1717 [PubMed:8294419]
[show Abstract]
We have measured the fidelity of leading and lagging strand DNA replication in HeLa cell extracts. Providing an excess of one dNTP in reactions induces replication errors consistent with misincorporation of that dNTP. With excess dTTP, both substitutions and single-nucleotide frameshifts are induced. Error distribution is nonrandom; reproducible hot spots for a substitution and a frameshift error are observed. Measurements with two vectors having the origin of replication on opposite sides of the mutational target demonstrate that error rates for G.dTTP and C.dTTP mispairs depend on whether the strand is replicated as the leading or lagging strand. Also, the two hot spots are only observed in one origin-target orientation. Replication reactions reconstituted from two fractions derived from extracts are 3-fold less accurate, but the error specificity with excess dTTP is similar to that with extracts. This suggests that the processes responsible for the nonrandom error rates are not lost as a result of fractionation. Furthermore, the reconstituted system is devoid of mismatch repair activity. Thus, mismatch repair is not responsible for the mispair-, site-, and strand-specific differences observed. | Satav JG, Modak MJ, Studzinski GP (1990)
Photoaffinity labeling of human c-myc protein with deoxythymidine triphosphate.
Laboratory investigation; a journal of technical methods and pathology 63, 551-556 [PubMed:2232707]
[show Abstract]
The recombinant human c-myc protein expressed in Escherichia coli can be efficiently labeled by ultraviolet-mediated cross-linking to dTTP and to a lesser extent to other nucleoside diphosphates and triphosphates, but not to nucleoside monophosphates. Specificity of nucleoside phosphate binding is suggested by (a) concentration-dependent competition by some nucleoside phosphates but not by others and (b) by the observation that the denatured myc protein does not bind the nucleotides. Competition experiments also indicate that the affinity of c-myc protein for nucleoside diphosphates and triphosphates is approximately the same irrespective of the nature of the base, or of the pentose sugar, but the thymine base permits the most efficient photoactivated cross-linking. The ultraviolet-mediated photoactivated cross-linking of deoxythymidine triphosphate has been used to identify the c-myc protein in extracts of cells which overexpress c-myc, and to identify the intermediates in myc oncoprotein degradation. | Aherne GW, Piall E, Aitkenhead S, Curtin N (1989)
A radioimmunoassay for deoxythymidine triphosphate.
Biochemical Society transactions 17, 1052 [PubMed:2628074] | McGowan JJ, Allen GP, Barnett JM, Gentry GA (1980)
Deoxythymidine kinase metabolism in equine herpesvirus type 3 infected horse embryo dermal fibroblasts.
Virology 101, 516-519 [PubMed:7361458] | Fox RM, Piddington SK, Tripp EH, Dudman NP, Tattersall MH (1979)
Thymidine sensitivity of cultured leukaemic lymphocytes.
Lancet (London, England) 2, 391-393 [PubMed:89451]
[show Abstract]
Cultured leukaemic lymphocytes from patients with T, null, or pre-B acute lymphoblastic leukaemia are shown to be highly sensitive to growth inhibition by thymidine. Thymidine sensitivity was correlated with reduced activity of the catabolic enzyme thymidine phosphorylase and sustained elevation of the deoxythymidine triphosphate pool after exposure to thymidine. It is suggested that thymidine may have a role in the management of certain acute lymphoblastic leukaemias of lymphomas. | Rossi M, Woodward DO (1975)
Enzymes of deoxythymidine triphosphate biosynthesis in Neurospora crassa mitochondria.
Journal of bacteriology 121, 640-647 [PubMed:163227]
[show Abstract]
Intact mitochondria of Neurospora crassa incorporate deoxythymidine 5'-monophosphate (dTMP) into deoxyribonucleic acid but not the label from (methyl-3H) deoxythymidine. Mitochondrial homogenates contain deoxythymidylate kinase (EC 2.7.4.9), deoxycytidylate aminohydrolase (dCMP deaminase) (EC 3.5.4.12), and thymidylate synthetase (EC 2.1.1b), but not thymidine kinase (EC 2.7.1.21) activity. dTMP kinase is loosely bound to the mitochondrial membrane and is solubilized by 0.4 M KCl in mitochondrial homogenates, the dCMP aminohydrolase deaminase) is bound to the inner membrane and is not solubilized by 0.4 M KCl. dTMP synthetase activity is found in the 2,000 times g particulate fractions by homogenization of mitochondria in 0.4 M KCl. The dCMP deaminase activity found in the particulate fraction of the inner membrane is efficiently regulated by the products of the pathway: deoxycytidine 5'-triphosphate activates whereas deoxythymidine 5'-triphosphate inhibits, as found for the soluble enzyme from other sources. These data indicate that mitochondria of N. crassa contain specific enzymes for the biosynthesis of deoxythymidine triphosphate. | Klose J, Flickinger RA (1972)
Incorporation of deoxythymidine triphosphate into DNA of fractions of mouse liver in vitro.
Experimental cell research 73, 236-239 [PubMed:4556566] |
|
