1g3u: Difference between revisions

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New page: left|200px<br /><applet load="1g3u" size="450" color="white" frame="true" align="right" spinBox="true" caption="1g3u, resolution 1.95Å" /> '''CRYSTAL STRUCTURE OF...
 
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[[Image:1g3u.jpg|left|200px]]<br /><applet load="1g3u" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1g3u, resolution 1.95&Aring;" />
'''CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP)'''<br />


==Overview==
==CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP)==
The X-ray structure of Mycobacterium tuberculosis TMP kinase at 1.95 A, resolution is described as a binary complex with its natural substrate, TMP. Its main features involve: (i) a clear magnesium-binding site; (ii), an alpha-helical conformation for the so-called LID region; and (iii) a, high density of positive charges in the active site. There is a network of, interactions involving highly conserved side-chains of the protein, the, magnesium ion, a sulphate ion mimicking the beta phosphate group of ATP, and the TMP molecule itself. All these interactions conspire in, stabilizing what appears to be the closed form of the enzyme. A complete, multialignment of all (32) known sequences of TMP kinases is presented., Subtle differences in the TMP binding site were noted, as compared to the, Escherichia coli, yeast and human enzyme structures, which have been, reported recently. These differences could be used to design specific, inhibitors of this essential enzyme of nucleotide metabolism. Two cases of, compensatory mutations were detected in the TMP binding site of eukaryotic, and prokaryotic enzymes. In addition, an intriguing high value of the, electric field is reported in the vicinity of the phosphate group of TMP, and the putative binding site of the gamma phosphate group of ATP.
<StructureSection load='1g3u' size='340' side='right'caption='[[1g3u]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1g3u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G3U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G3U FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TMP:THYMIDINE-5-PHOSPHATE'>TMP</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1g3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g3u OCA], [https://pdbe.org/1g3u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1g3u RCSB], [https://www.ebi.ac.uk/pdbsum/1g3u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1g3u ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/KTHY_MYCTU KTHY_MYCTU] Catalyzes the reversible phosphorylation of deoxythymidine monophosphate (dTMP) to deoxythymidine diphosphate (dTDP), using ATP as its preferred phosphoryl donor. Situated at the junction of both de novo and salvage pathways of deoxythymidine triphosphate (dTTP) synthesis, is essential for DNA synthesis and cellular growth. Has a broad specificity for nucleoside triphosphates, being highly active with ATP or dATP as phosphate donors, and less active with ITP, GTP, CTP and UTP.[HAMAP-Rule:MF_00165]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g3/1g3u_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1g3u ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1G3U is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] with SO4, MG and TMP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/dTMP_kinase dTMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.9 2.7.4.9] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1G3U OCA].
*[[Thymidylate kinase 3D structures|Thymidylate kinase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
X-ray structure of TMP kinase from Mycobacterium tuberculosis complexed with TMP at 1.95 A resolution., Li de la Sierra I, Munier-Lehmann H, Gilles AM, Barzu O, Delarue M, J Mol Biol. 2001 Aug 3;311(1):87-100. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11469859 11469859]
[[Category: Large Structures]]
[[Category: Mycobacterium tuberculosis]]
[[Category: Mycobacterium tuberculosis]]
[[Category: Single protein]]
[[Category: Barzu O]]
[[Category: dTMP kinase]]
[[Category: Delarue M]]
[[Category: Barzu, O.]]
[[Category: Gilles AM]]
[[Category: Delarue, M.]]
[[Category: Li de la Sierra I]]
[[Category: Gilles, A.M.]]
[[Category: Munier-Lehmann H]]
[[Category: Munier-Lehmann, H.]]
[[Category: Sierra, I.Li.de.la.]]
[[Category: MG]]
[[Category: SO4]]
[[Category: TMP]]
[[Category: kinase]]
[[Category: transferase (atp:tmp phosphotransferase)]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 15:40:43 2007''

Latest revision as of 10:22, 7 February 2024

CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP)CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP)

Structural highlights

1g3u is a 1 chain structure with sequence from Mycobacterium tuberculosis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.95Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

KTHY_MYCTU Catalyzes the reversible phosphorylation of deoxythymidine monophosphate (dTMP) to deoxythymidine diphosphate (dTDP), using ATP as its preferred phosphoryl donor. Situated at the junction of both de novo and salvage pathways of deoxythymidine triphosphate (dTTP) synthesis, is essential for DNA synthesis and cellular growth. Has a broad specificity for nucleoside triphosphates, being highly active with ATP or dATP as phosphate donors, and less active with ITP, GTP, CTP and UTP.[HAMAP-Rule:MF_00165]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1g3u, resolution 1.95Å

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