View source for 3gru


==Crystal Structure of the Complex between AMP and Methanocaldococcus jannaschi Dim1==
<StructureSection load='3gru' size='340' side='right'caption='[[3gru]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3gru]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GRU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GRU 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]] 1.6&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=3gru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gru OCA], [https://pdbe.org/3gru PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gru RCSB], [https://www.ebi.ac.uk/pdbsum/3gru PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gru ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RSMA_METJA RSMA_METJA] Specifically dimethylates two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits.[HAMAP-Rule:MF_00607]<ref>PMID:19520088</ref> <ref>PMID:20163168</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/gr/3gru_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=3gru ConSurf].
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== Publication Abstract from PubMed ==
The KsgA/Dim1 family of proteins is intimately involved in ribosome biogenesis in all organisms. These enzymes share the common function of dimethylating two adenosine residues near the 3'-OH end of the small subunit rRNA; orthologs in the three kingdoms, along with eukaryotic organelles, have evolved additional functions in rRNA processing, ribosome assembly, and, surprisingly, transcription in mitochondria. The methyltransferase reaction is intriguingly elaborate. The enzymes can bind to naked small subunit rRNA but cannot methylate their target bases until a subset of ribosomal proteins have bound and the nascent subunit has reached a certain level of maturity. Once this threshold is reached, the enzyme must stabilize two adenosines into the active site at separate times and two methyl groups must be transferred to each adenosine, with concomitant exchanges of the product S-adenosyl-l-homocysteine and the methyl donor substrate S-adenosyl-l-methionine. A detailed molecular understanding of this mechanism is currently lacking. Structural analysis of the interactions between the enzyme and substrate will aid in this understanding. Here we present the structure of KsgA from Methanocaldococcus jannaschii in complex with several ligands, including the first structure of S-adenosyl-l-methionine bound to a KsgA/Dim1 enzyme in a catalytically productive way. We also discuss the inability thus far to determine a structure of a target adenosine bound in its active site.

Binding of adenosine-based ligands to the MjDim1 rRNA methyltransferase: implications for reaction mechanism and drug design.,O'Farrell HC, Musayev FN, Scarsdale JN, Rife JP Biochemistry. 2010 Mar 30;49(12):2697-704. PMID:20163168<ref>PMID:20163168</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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==See Also==
*[[Adenosine dimethyltransferase 3D structures|Adenosine dimethyltransferase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: Musayev FN]]
[[Category: Rife JP]]
[[Category: Scarsdale JN]]