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1xzq

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[[Image:1xzq.gif|left|200px]]<br /><applet load="1xzq" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1xzq, resolution 2.9&Aring;" />
 
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'''Structure of the GTP-binding protein TrmE from Thermotoga maritima complexed with 5-formyl-THF'''<br />
 
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==Overview==
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==Structure of the GTP-binding protein TrmE from Thermotoga maritima complexed with 5-formyl-THF==
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TrmE is a 50 kDa guanine nucleotide-binding protein conserved between bacteria and man. It is involved in the modification of uridine bases (U34) at the first anticodon (wobble) position of tRNAs decoding two-family box triplets. The precise role of TrmE in the modification reaction is hitherto unknown. Here, we report the X-ray structure of TrmE from Thermotoga maritima. The structure reveals a three-domain protein comprising the N-terminal alpha/beta domain, the central helical domain and the G domain, responsible for GTP binding and hydrolysis. The N-terminal domain induces dimerization and is homologous to the tetrahydrofolate-binding domain of N,N-dimethylglycine oxidase. Biochemical and structural studies show that TrmE indeed binds formyl-tetrahydrofolate. A cysteine residue, necessary for modification of U34, is located close to the C1-group donor 5-formyl-tetrahydrofolate, suggesting a direct role of TrmE in the modification analogous to DNA modification enzymes. We propose a reaction mechanism whereby TrmE actively participates in the formylation reaction of uridine and regulates the ensuing hydrogenation reaction of a Schiff's base intermediate.
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<StructureSection load='1xzq' size='340' side='right'caption='[[1xzq]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1xzq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XZQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XZQ FirstGlance]. <br>
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1XZQ is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima] with <scene name='pdbligand=FON:'>FON</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XZQ OCA].
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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]] 2.9&#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=FON:N-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}-L-GLUTAMIC+ACID'>FON</scene></td></tr>
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==Reference==
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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=1xzq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xzq OCA], [https://pdbe.org/1xzq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xzq RCSB], [https://www.ebi.ac.uk/pdbsum/1xzq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xzq ProSAT]</span></td></tr>
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The structure of the TrmE GTP-binding protein and its implications for tRNA modification., Scrima A, Vetter IR, Armengod ME, Wittinghofer A, EMBO J. 2005 Jan 12;24(1):23-33. Epub 2004 Dec 16. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15616586 15616586]
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</table>
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[[Category: Protein complex]]
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== Function ==
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[https://www.uniprot.org/uniprot/MNME_THEMA MNME_THEMA] Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34.
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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/xz/1xzq_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=1xzq ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Thermotoga maritima]]
[[Category: Thermotoga maritima]]
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[[Category: Armengod, M E.]]
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[[Category: Armengod ME]]
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[[Category: Scrima, A.]]
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[[Category: Scrima A]]
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[[Category: Vetter, I R.]]
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[[Category: Vetter IR]]
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[[Category: Wittinghofer, A.]]
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[[Category: Wittinghofer A]]
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[[Category: FON]]
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[[Category: gtp-binding]]
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[[Category: thf-binding]]
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[[Category: trna-modification]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:00:25 2008''
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Current revision

Structure of the GTP-binding protein TrmE from Thermotoga maritima complexed with 5-formyl-THF

PDB ID 1xzq

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