1dl5

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(New page: 200px<br /><applet load="1dl5" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dl5, resolution 1.8&Aring;" /> '''PROTEIN-L-ISOASPARTAT...)
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[[Image:1dl5.gif|left|200px]]<br /><applet load="1dl5" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1dl5, resolution 1.8&Aring;" />
 
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'''PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE'''<br />
 
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==Overview==
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==PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE==
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BACKGROUND: Formation of isoaspartyl residues is one of several processes, that damage proteins as they age. Protein L-isoaspartate (D-aspartate), O-methyltransferase (PIMT) is a conserved and nearly ubiquitous enzyme, that catalyzes the repair of proteins damaged by isoaspartyl formation., RESULTS: We have determined the first structure of a PIMT from crystals of, the T. maritima enzyme complexed to S-adenosyl-L-homocysteine (AdoHcy) and, refined it to 1.8 A resolution. Although PIMT forms one structural unit, the protein can be divided functionally into three subdomains. The central, subdomain closely resembles other S-adenosyl-L-methionine-dependent, methyltransferases but bears a striking alteration of topological, connectivity, which is not shared by any other member of this family., Rather than arranged as a mixed beta sheet with topology 6 upward arrow7, downward arrow5 upward arrow4 upward arrow1 upward arrow2 upward arrow3, upward arrow, the central sheet of PIMT is reorganized to 7 upward arrow6, downward arrow5 upward arrow4 upward arrow1 upward arrow2 upward arrow3, upward arrow. AdoHcy is largely buried between the N-terminal and central, subdomains by a conserved and largely hydrophobic loop on one rim of the, binding cleft, and a conserved Ser/Thr-rich beta strand on the other. The, Ser/Thr-rich strand may provide hydrogen bonds for specific interactions, with isoaspartyl substrates. The side chain of Ile-206, a conserved, residue, crosses the cleft, restricting access to the donor methyl group, to a deep well, the putative isoaspartyl methyl acceptor site., CONCLUSIONS: The structure of PIMT reveals a unique modification of the, methyltransferase fold along with a site for specific recognition of, isoaspartyl substrates. The sequence conservation among PIMTs suggests, that the current structure should prove a reliable model for understanding, the repair of isoaspartyl damage in all organisms.
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<StructureSection load='1dl5' size='340' side='right'caption='[[1dl5]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1dl5]] is a 2 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=1DL5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DL5 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dl5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dl5 OCA], [https://pdbe.org/1dl5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dl5 RCSB], [https://www.ebi.ac.uk/pdbsum/1dl5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dl5 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PIMT_THEMA PIMT_THEMA] Catalyzes the methyl esterification of L-isoaspartyl residues in peptides and proteins that result from spontaneous decomposition of normal L-aspartyl and L-asparaginyl residues. It plays a role in the repair and/or degradation of damaged proteins.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dl/1dl5_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1dl5 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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BACKGROUND: Formation of isoaspartyl residues is one of several processes that damage proteins as they age. Protein L-isoaspartate (D-aspartate) O-methyltransferase (PIMT) is a conserved and nearly ubiquitous enzyme that catalyzes the repair of proteins damaged by isoaspartyl formation. RESULTS: We have determined the first structure of a PIMT from crystals of the T. maritima enzyme complexed to S-adenosyl-L-homocysteine (AdoHcy) and refined it to 1.8 A resolution. Although PIMT forms one structural unit, the protein can be divided functionally into three subdomains. The central subdomain closely resembles other S-adenosyl-L-methionine-dependent methyltransferases but bears a striking alteration of topological connectivity, which is not shared by any other member of this family. Rather than arranged as a mixed beta sheet with topology 6 upward arrow7 downward arrow5 upward arrow4 upward arrow1 upward arrow2 upward arrow3 upward arrow, the central sheet of PIMT is reorganized to 7 upward arrow6 downward arrow5 upward arrow4 upward arrow1 upward arrow2 upward arrow3 upward arrow. AdoHcy is largely buried between the N-terminal and central subdomains by a conserved and largely hydrophobic loop on one rim of the binding cleft, and a conserved Ser/Thr-rich beta strand on the other. The Ser/Thr-rich strand may provide hydrogen bonds for specific interactions with isoaspartyl substrates. The side chain of Ile-206, a conserved residue, crosses the cleft, restricting access to the donor methyl group to a deep well, the putative isoaspartyl methyl acceptor site. CONCLUSIONS: The structure of PIMT reveals a unique modification of the methyltransferase fold along with a site for specific recognition of isoaspartyl substrates. The sequence conservation among PIMTs suggests that the current structure should prove a reliable model for understanding the repair of isoaspartyl damage in all organisms.
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==About this Structure==
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Crystal structure of protein isoaspartyl methyltransferase: a catalyst for protein repair.,Skinner MM, Puvathingal JM, Walter RL, Friedman AM Structure. 2000 Nov 15;8(11):1189-201. PMID:11080641<ref>PMID:11080641</ref>
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1DL5 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima] with CD, CL and SAH as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Protein-L-isoaspartate(D-aspartate)_O-methyltransferase Protein-L-isoaspartate(D-aspartate) O-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.77 2.1.1.77] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DL5 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Crystal structure of protein isoaspartyl methyltransferase: a catalyst for protein repair., Skinner MM, Puvathingal JM, Walter RL, Friedman AM, Structure. 2000 Nov 15;8(11):1189-201. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11080641 11080641]
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</div>
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[[Category: Protein-L-isoaspartate(D-aspartate) O-methyltransferase]]
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<div class="pdbe-citations 1dl5" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Thermotoga maritima]]
[[Category: Thermotoga maritima]]
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[[Category: Friedman, A.M.]]
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[[Category: Friedman AM]]
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[[Category: Puvathingal, J.M.]]
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[[Category: Puvathingal JM]]
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[[Category: Skinner, M.M.]]
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[[Category: Skinner MM]]
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[[Category: Walter, R.L.]]
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[[Category: Walter RL]]
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[[Category: CD]]
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[[Category: CL]]
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[[Category: SAH]]
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[[Category: deamidation]]
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[[Category: isoaspartyl residues]]
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[[Category: methyltransferase]]
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[[Category: post-translational modification]]
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[[Category: protein repair]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:22:52 2007''
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Current revision

PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE

PDB ID 1dl5

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