View source for 2plm


==Crystal structure of the protein TM0936 from Thermotoga maritima complexed with ZN and S-inosylhomocysteine==
<StructureSection load='2plm' size='340' side='right'caption='[[2plm]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2plm]] is a 1 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=2PLM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PLM 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]] 2.1&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SIB:(2S)-2-AMINO-4-({[(2S,3S,4R,5R)-3,4-DIHYDROXY-5-(6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)TETRAHYDROFURAN-2-YL]METHYL}THIO)BUTANOIC+ACID'>SIB</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2plm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2plm OCA], [https://pdbe.org/2plm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2plm RCSB], [https://www.ebi.ac.uk/pdbsum/2plm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2plm ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/2plm TOPSAN]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/MTAD_THEMA MTAD_THEMA] Catalyzes the deamination of 5-methylthioadenosine and S-adenosyl-L-homocysteine into 5-methylthioinosine and S-inosyl-L-homocysteine, respectively. Is also able to deaminate adenosine. Adenosine-5-monophosphate (AMP) and S-adenosyl-L-methionine (SAM) are not enzyme substrates.<ref>PMID:17603473</ref> 
== 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/pl/2plm_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=2plm ConSurf].
<div style="clear:both"></div>
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== Publication Abstract from PubMed ==
With many genomes sequenced, a pressing challenge in biology is predicting the function of the proteins that the genes encode. When proteins are unrelated to others of known activity, bioinformatics inference for function becomes problematic. It would thus be useful to interrogate protein structures for function directly. Here, we predict the function of an enzyme of unknown activity, Tm0936 from Thermotoga maritima, by docking high-energy intermediate forms of thousands of candidate metabolites. The docking hit list was dominated by adenine analogues, which appeared to undergo C6-deamination. Four of these, including 5-methylthioadenosine and S-adenosylhomocysteine (SAH), were tested as substrates, and three had substantial catalytic rate constants (10(5) M(-1 )s(-1)). The X-ray crystal structure of the complex between Tm0936 and the product resulting from the deamination of SAH, S-inosylhomocysteine, was determined, and it corresponded closely to the predicted structure. The deaminated products can be further metabolized by T. maritima in a previously uncharacterized SAH degradation pathway. Structure-based docking with high-energy forms of potential substrates may be a useful tool to annotate enzymes for function.

Structure-based activity prediction for an enzyme of unknown function.,Hermann JC, Marti-Arbona R, Fedorov AA, Fedorov E, Almo SC, Shoichet BK, Raushel FM Nature. 2007 Aug 16;448(7155):775-9. Epub 2007 Jul 1. PMID:17603473<ref>PMID:17603473</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 2plm" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Thermotoga maritima]]
[[Category: Almo SC]]
[[Category: Fedorov AA]]
[[Category: Fedorov EV]]
[[Category: Hermann JC]]
[[Category: Marti-Arbona R]]
[[Category: Raushel FM]]
[[Category: Shoichet BK]]