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| | ==2.1 Angstrom crystal structure of the L114P mutant of E. Coli KsgA== | | ==2.1 Angstrom crystal structure of the L114P mutant of E. Coli KsgA== |
| - | <StructureSection load='3tpz' size='340' side='right' caption='[[3tpz]], [[Resolution|resolution]] 2.10Å' scene=''> | + | <StructureSection load='3tpz' size='340' side='right'caption='[[3tpz]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3tpz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TPZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TPZ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3tpz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TPZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TPZ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1qyr|1qyr]], [[2fyc|2fyc]], [[3fyd|3fyd]], [[3fut|3fut]], [[3ftd|3ftd]], [[1qam|1qam]]</td></tr> | + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1qyr|1qyr]], [[2fyc|2fyc]], [[3fyd|3fyd]], [[3fut|3fut]], [[3ftd|3ftd]], [[1qam|1qam]]</div></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b0051, JW0050, ksgA, rsmA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr> | + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b0051, JW0050, ksgA, rsmA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/16S_rRNA_(adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.182 2.1.1.182] </span></td></tr> | + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/16S_rRNA_(adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.182 2.1.1.182] </span></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=3tpz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tpz OCA], [http://pdbe.org/3tpz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3tpz RCSB], [http://www.ebi.ac.uk/pdbsum/3tpz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3tpz 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=3tpz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tpz OCA], [https://pdbe.org/3tpz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tpz RCSB], [https://www.ebi.ac.uk/pdbsum/3tpz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tpz ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RSMA_ECOLI RSMA_ECOLI]] Specifically dimethylates two adjacent adenosines (A1518 and A1519) 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. Has also a DNA glycosylase/AP lyase activity that removes C mispaired with oxidized T from DNA, and may play a role in protection of DNA against oxidative stress.<ref>PMID:3905517</ref> <ref>PMID:19223326</ref> <ref>PMID:18990185</ref> | + | [[https://www.uniprot.org/uniprot/RSMA_ECOLI RSMA_ECOLI]] Specifically dimethylates two adjacent adenosines (A1518 and A1519) 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. Has also a DNA glycosylase/AP lyase activity that removes C mispaired with oxidized T from DNA, and may play a role in protection of DNA against oxidative stress.<ref>PMID:3905517</ref> <ref>PMID:19223326</ref> <ref>PMID:18990185</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[Adenosine dimethyltransferase|Adenosine dimethyltransferase]] | + | *[[Adenosine dimethyltransferase 3D structures|Adenosine dimethyltransferase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Ecoli]] | | [[Category: Ecoli]] |
| | + | [[Category: Large Structures]] |
| | [[Category: Musayev, F N]] | | [[Category: Musayev, F N]] |
| | [[Category: Rife, J P]] | | [[Category: Rife, J P]] |
| Structural highlights
3tpz is a 2 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Ligands: | , |
| Related: | |
| Gene: | b0051, JW0050, ksgA, rsmA (ECOLI) |
| Activity: | 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase, with EC number 2.1.1.182 |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
[RSMA_ECOLI] Specifically dimethylates two adjacent adenosines (A1518 and A1519) 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. Has also a DNA glycosylase/AP lyase activity that removes C mispaired with oxidized T from DNA, and may play a role in protection of DNA against oxidative stress.[1] [2] [3]
Publication Abstract from PubMed
The KsgA methyltransferase is universally conserved and plays a key role in regulating ribosome biogenesis. KsgA has a complex reaction mechanism, transferring a total of four methyl groups onto two separate adenosine residues, A1518 and A1519, in the small subunit rRNA. This means that the active site pocket must accept both adenosine and N(6)-methyladenosine as substrates to catalyze formation of the final product N(6),N(6)-dimethyladenosine. KsgA is related to DNA adenosine methyltransferases, which transfer only a single methyl group to their target adenosine residue. We demonstrate that part of the discrimination between mono- and dimethyltransferase activity lies in a single residue in the active site, L114; this residue is part of a conserved motif, known as motif IV, which is common to a large group of S-adenosyl-l-methionine-dependent methyltransferases. Mutation of the leucine to a proline mimics the sequence found in DNA methyltransferases. The L114P mutant of KsgA shows diminished overall activity, and its ability to methylate the N(6)-methyladenosine intermediate to produce N(6),N(6)-dimethyladenosine is impaired; this is in contrast to a second active site mutation, N113A, which diminishes activity to a level comparable to L114P without affecting the methylation of N(6)-methyladenosine. We discuss the implications of this work for understanding the mechanism of KsgA's multiple catalytic steps.
Control of Substrate Specificity by a Single Active Site Residue of the KsgA Methyltransferase.,O'Farrell HC, Musayev FN, Scarsdale JN, Rife JP Biochemistry. 2012 Jan 10;51(1):466-74. Epub 2011 Dec 22. PMID:22142337[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ van Buul CP, van Knippenberg PH. Nucleotide sequence of the ksgA gene of Escherichia coli: comparison of methyltransferases effecting dimethylation of adenosine in ribosomal RNA. Gene. 1985;38(1-3):65-72. PMID:3905517
- ↑ Zhang-Akiyama QM, Morinaga H, Kikuchi M, Yonekura S, Sugiyama H, Yamamoto K, Yonei S. KsgA, a 16S rRNA adenine methyltransferase, has a novel DNA glycosylase/AP lyase activity to prevent mutations in Escherichia coli. Nucleic Acids Res. 2009 Apr;37(7):2116-25. doi: 10.1093/nar/gkp057. Epub 2009 Feb, 17. PMID:19223326 doi:10.1093/nar/gkp057
- ↑ Connolly K, Rife JP, Culver G. Mechanistic insight into the ribosome biogenesis functions of the ancient protein KsgA. Mol Microbiol. 2008 Dec;70(5):1062-75. doi: 10.1111/j.1365-2958.2008.06485.x. PMID:18990185 doi:10.1111/j.1365-2958.2008.06485.x
- ↑ O'Farrell HC, Musayev FN, Scarsdale JN, Rife JP. Control of Substrate Specificity by a Single Active Site Residue of the KsgA Methyltransferase. Biochemistry. 2012 Jan 10;51(1):466-74. Epub 2011 Dec 22. PMID:22142337 doi:10.1021/bi201539j
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