3mf2: Difference between revisions
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< | ==Crystal structure of class II aaRS homologue (Bll0957) complexed with AMP== | ||
<StructureSection load='3mf2' size='340' side='right'caption='[[3mf2]], [[Resolution|resolution]] 2.15Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3mf2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bradyrhizobium_diazoefficiens_USDA_110 Bradyrhizobium diazoefficiens USDA 110]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MF2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MF2 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]] 2.15Å</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=GOL:GLYCEROL'>GOL</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=3mf2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mf2 OCA], [https://pdbe.org/3mf2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3mf2 RCSB], [https://www.ebi.ac.uk/pdbsum/3mf2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3mf2 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/AACL1_BRADU AACL1_BRADU] Catalyzes the ATP-dependent activation of L-glycine and its transfer to the phosphopantetheine prosthetic group covalently attached to the vicinal carrier protein bsr0959 of yet unknown function. May participate in nonribosomal peptide synthesis or related processes. L-alanine is a poor substrate whereas L-serine or D-amino acids are not substrates for ATP-dependent activation. Does not display tRNA aminoacylation activity.<ref>PMID:20663952</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/mf/3mf2_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3mf2 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Aminoacyl-tRNA synthetases (aaRSs) are ancient and evolutionary conserved enzymes catalyzing the formation of aminoacyl-tRNAs, that are used as substrates for ribosomal protein biosynthesis. In addition to full length aaRS genes, genomes of many organisms are sprinkled with truncated genes encoding single-domain aaRS-like proteins, which often have relinquished their canonical role in genetic code translation. We have identified the genes for putative seryl-tRNA synthetase homologs widespread in bacterial genomes and characterized three of them biochemically and structurally. The proteins encoded are homologous to the catalytic domain of highly diverged, atypical seryl-tRNA synthetases (aSerRSs) found only in methanogenic archaea and are deprived of the tRNA-binding domain. Remarkably, in comparison to SerRSs, aSerRS homologs display different and relaxed amino acid specificity. aSerRS homologs lack canonical tRNA aminoacylating activity and instead transfer activated amino acid to phosphopantetheine prosthetic group of putative carrier proteins, whose genes were identified in the genomic surroundings of aSerRS homologs. Detailed kinetic analysis confirmed that aSerRS homologs aminoacylate these carrier proteins efficiently and specifically. Accordingly, aSerRS homologs were renamed amino acid:[carrier protein] ligases (AMP forming). The enzymatic activity of aSerRS homologs is reminiscent of adenylation domains in nonribosomal peptide synthesis, and thus they represent an intriguing link between programmable ribosomal protein biosynthesis and template-independent nonribosomal peptide synthesis. | |||
Homologs of aminoacyl-tRNA synthetases acylate carrier proteins and provide a link between ribosomal and nonribosomal peptide synthesis.,Mocibob M, Ivic N, Bilokapic S, Maier T, Luic M, Ban N, Weygand-Durasevic I Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14585-90. Epub 2010 Jul 27. PMID:20663952<ref>PMID:20663952</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3mf2" style="background-color:#fffaf0;"></div> | |||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
[[Category: Bradyrhizobium | </StructureSection> | ||
[[Category: Ban | [[Category: Bradyrhizobium diazoefficiens USDA 110]] | ||
[[Category: Bilokapic | [[Category: Large Structures]] | ||
[[Category: Ivic | [[Category: Ban N]] | ||
[[Category: Luic | [[Category: Bilokapic S]] | ||
[[Category: Maier | [[Category: Ivic N]] | ||
[[Category: Mocibob | [[Category: Luic M]] | ||
[[Category: Weygand-Durasevic | [[Category: Maier T]] | ||
[[Category: Mocibob M]] | |||
[[Category: Weygand-Durasevic I]] | |||
Latest revision as of 11:03, 9 October 2024
Crystal structure of class II aaRS homologue (Bll0957) complexed with AMPCrystal structure of class II aaRS homologue (Bll0957) complexed with AMP
Structural highlights
FunctionAACL1_BRADU Catalyzes the ATP-dependent activation of L-glycine and its transfer to the phosphopantetheine prosthetic group covalently attached to the vicinal carrier protein bsr0959 of yet unknown function. May participate in nonribosomal peptide synthesis or related processes. L-alanine is a poor substrate whereas L-serine or D-amino acids are not substrates for ATP-dependent activation. Does not display tRNA aminoacylation activity.[1] 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 PubMedAminoacyl-tRNA synthetases (aaRSs) are ancient and evolutionary conserved enzymes catalyzing the formation of aminoacyl-tRNAs, that are used as substrates for ribosomal protein biosynthesis. In addition to full length aaRS genes, genomes of many organisms are sprinkled with truncated genes encoding single-domain aaRS-like proteins, which often have relinquished their canonical role in genetic code translation. We have identified the genes for putative seryl-tRNA synthetase homologs widespread in bacterial genomes and characterized three of them biochemically and structurally. The proteins encoded are homologous to the catalytic domain of highly diverged, atypical seryl-tRNA synthetases (aSerRSs) found only in methanogenic archaea and are deprived of the tRNA-binding domain. Remarkably, in comparison to SerRSs, aSerRS homologs display different and relaxed amino acid specificity. aSerRS homologs lack canonical tRNA aminoacylating activity and instead transfer activated amino acid to phosphopantetheine prosthetic group of putative carrier proteins, whose genes were identified in the genomic surroundings of aSerRS homologs. Detailed kinetic analysis confirmed that aSerRS homologs aminoacylate these carrier proteins efficiently and specifically. Accordingly, aSerRS homologs were renamed amino acid:[carrier protein] ligases (AMP forming). The enzymatic activity of aSerRS homologs is reminiscent of adenylation domains in nonribosomal peptide synthesis, and thus they represent an intriguing link between programmable ribosomal protein biosynthesis and template-independent nonribosomal peptide synthesis. Homologs of aminoacyl-tRNA synthetases acylate carrier proteins and provide a link between ribosomal and nonribosomal peptide synthesis.,Mocibob M, Ivic N, Bilokapic S, Maier T, Luic M, Ban N, Weygand-Durasevic I Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14585-90. Epub 2010 Jul 27. PMID:20663952[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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