1n5i

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[[Image:1n5i.gif|left|200px]]<br /><applet load="1n5i" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1n5i, resolution 1.85&Aring;" />
 
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'''CRYSTAL STRUCTURE OF INACTIVE MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP) AT PH 4.6 (RESOLUTION 1.85 A)'''<br />
 
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==Overview==
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==CRYSTAL STRUCTURE OF INACTIVE MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP) AT PH 4.6 (RESOLUTION 1.85 A)==
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Mycobacterium tuberculosis TMP kinase (TMPK(Mtub)) represents a promising target for developing drugs against tuberculosis because the configuration of its active site is unique in the TMPK family. To help elucidate the phosphorylation mechanism employed by this enzyme, structural changes occurring upon binding of substrates and subsequent catalysis were investigated by protein crystallography. Six new structures of TMPK(Mtub) were solved at a resolution better than 2.3A, including the first structure of an apo-TMPK, obtained by triggering catalysis in a crystal of a TMPK(Mtub)-TMP complex, which resulted in the release of the TDP product. A series of snapshots along the reaction pathway is obtained, revealing the closure of the active site in going from an empty to a fully occupied state, suggestive of an induced-fit mechanism typical of NMPKs. However, in TMPK(Mtub) the LID closure couples to the binding with an unusual location for a magnesium ion coordinating TMP in the active site. Our data suggest strongly that this ion is required for catalysis, acting as a clamp, possibly in concert with Arg95, to neutralise electrostatic repulsion between the anionic substrates, optimise their proper alignment and activate them through direct and water-mediated interactions. The 3'-hydroxyl moiety of TMP, critical to metal stabilisation, appears to be a target of choice for the design of potent inhibitors. On the other hand, the usual NTP-bound magnesium is not seen in our structures and Arg14, a P-loop residue unique to TMPK(Mtub), may take over its role. Therefore, TMPK(Mtub) seems to have swapped the use of a metal ion as compared with e.g. human TMPK. Finally, TTP was observed in crystals of TMPK(Mtub), locked by Arg14, thus providing a structural explanation for the observed inhibitory effect of TTP putatively involved in a mechanism of feedback regulation of the enzymatic activity.
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<StructureSection load='1n5i' size='340' side='right'caption='[[1n5i]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1n5i]] 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=1N5I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N5I FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TMP:THYMIDINE-5-PHOSPHATE'>TMP</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1n5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n5i OCA], [https://pdbe.org/1n5i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n5i RCSB], [https://www.ebi.ac.uk/pdbsum/1n5i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n5i ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n5/1n5i_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1n5i ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1N5I 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 <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=FLC:'>FLC</scene>, <scene name='pdbligand=TMP:'>TMP</scene> and <scene name='pdbligand=ATP:'>ATP</scene> 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1N5I OCA].
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*[[Thymidylate kinase 3D structures|Thymidylate kinase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Mycobacterium tuberculosis thymidylate kinase: structural studies of intermediates along the reaction pathway., Fioravanti E, Haouz A, Ursby T, Munier-Lehmann H, Delarue M, Bourgeois D, J Mol Biol. 2003 Apr 11;327(5):1077-92. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12662932 12662932]
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[[Category: Large Structures]]
[[Category: Mycobacterium tuberculosis]]
[[Category: Mycobacterium tuberculosis]]
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[[Category: Single protein]]
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[[Category: Bourgeois D]]
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[[Category: dTMP kinase]]
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[[Category: Delarue M]]
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[[Category: Bourgeois, D.]]
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[[Category: Fioravanti E]]
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[[Category: Delarue, M.]]
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[[Category: Haouz A]]
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[[Category: Fioravanti, E.]]
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[[Category: Munier-Lehmann H]]
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[[Category: Haouz, A.]]
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[[Category: Ursby T]]
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[[Category: Munier-Lehmann, H.]]
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[[Category: Ursby, T.]]
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[[Category: ATP]]
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[[Category: FLC]]
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[[Category: SO4]]
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[[Category: TMP]]
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[[Category: kinase]]
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[[Category: transferase (atp:tmp phosphotransferase)]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:02:26 2008''
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Current revision

CRYSTAL STRUCTURE OF INACTIVE MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP) AT PH 4.6 (RESOLUTION 1.85 A)

PDB ID 1n5i

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