|
|
| Line 1: |
Line 1: |
| | | | |
| | ==Crystal Structure of the Complex between AMP and Methanocaldococcus jannaschi Dim1== | | ==Crystal Structure of the Complex between AMP and Methanocaldococcus jannaschi Dim1== |
| - | <StructureSection load='3gru' size='340' side='right' caption='[[3gru]], [[Resolution|resolution]] 1.60Å' scene=''> | + | <StructureSection load='3gru' size='340' side='right'caption='[[3gru]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3gru]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GRU FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3gru]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. 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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3fyc|3fyc]], [[3fyd|3fyd]], [[1qyr|1qyr]], [[2h1r|2h1r]], [[1zq9|1zq9]], [[3fuv|3fuv]], [[3fut|3fut]], [[3fuu|3fuu]], [[3fux|3fux]], [[3fuw|3fuw]], [[3grr|3grr]], [[3grv|3grv]], [[3gry|3gry]]</td></tr> | + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3fyc|3fyc]], [[3fyd|3fyd]], [[1qyr|1qyr]], [[2h1r|2h1r]], [[1zq9|1zq9]], [[3fuv|3fuv]], [[3fut|3fut]], [[3fuu|3fuu]], [[3fux|3fux]], [[3fuw|3fuw]], [[3grr|3grr]], [[3grv|3grv]], [[3gry|3gry]]</div></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ksgA, MJ1029 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</td></tr> | + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ksgA, MJ1029 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3gru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gru OCA], [http://pdbe.org/3gru PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gru RCSB], [http://www.ebi.ac.uk/pdbsum/3gru PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3gru ProSAT]</span></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> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> | + | [[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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 32: |
Line 32: |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Adenosine dimethyltransferase|Adenosine dimethyltransferase]] | + | *[[Adenosine dimethyltransferase 3D structures|Adenosine dimethyltransferase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| Line 38: |
Line 38: |
| | </StructureSection> | | </StructureSection> |
| | [[Category: Atcc 43067]] | | [[Category: Atcc 43067]] |
| | + | [[Category: Large Structures]] |
| | [[Category: Musayev, F N]] | | [[Category: Musayev, F N]] |
| | [[Category: Rife, J P]] | | [[Category: Rife, J P]] |
| Structural highlights
3gru is a 1 chain structure with sequence from Atcc 43067. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Ligands: | , |
| Related: | 3fyc, 3fyd, 1qyr, 2h1r, 1zq9, 3fuv, 3fut, 3fuu, 3fux, 3fuw, 3grr, 3grv, 3gry |
| Gene: | ksgA, MJ1029 (ATCC 43067) |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
[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][1] [2]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
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[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Pulicherla N, Pogorzala LA, Xu Z, O Farrell HC, Musayev FN, Scarsdale JN, Sia EA, Culver GM, Rife JP. Structural and functional divergence within the Dim1/KsgA family of rRNA methyltransferases. J Mol Biol. 2009 Sep 4;391(5):884-93. Epub 2009 Jun 9. PMID:19520088 doi:10.1016/j.jmb.2009.06.015
- ↑ O'Farrell HC, Musayev FN, Scarsdale JN, Rife JP. Binding of adenosine-based ligands to the MjDim1 rRNA methyltransferase: implications for reaction mechanism and drug design. Biochemistry. 2010 Mar 30;49(12):2697-704. PMID:20163168 doi:10.1021/bi901875x
- ↑ O'Farrell HC, Musayev FN, Scarsdale JN, Rife JP. Binding of adenosine-based ligands to the MjDim1 rRNA methyltransferase: implications for reaction mechanism and drug design. Biochemistry. 2010 Mar 30;49(12):2697-704. PMID:20163168 doi:10.1021/bi901875x
|
