1jg3: Difference between revisions

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New page: left|200px<br /><applet load="1jg3" size="450" color="white" frame="true" align="right" spinBox="true" caption="1jg3, resolution 2.1Å" /> '''Crystal Structure of ...
 
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[[Image:1jg3.jpg|left|200px]]<br /><applet load="1jg3" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1jg3, resolution 2.1&Aring;" />
'''Crystal Structure of L-isoaspartyl (D-aspartyl) O-methyltransferase with adenosine & VYP(ISP)HA substrate'''<br />


==Overview==
==Crystal Structure of L-isoaspartyl (D-aspartyl) O-methyltransferase with adenosine & VYP(ISP)HA substrate==
Protein L-isoaspartyl (D-aspartyl) methyltransferases (EC 2.1.1.77) are, found in almost all organisms. These enzymes catalyze the, S-adenosylmethionine (AdoMet)-dependent methylation of isomerized and, racemized aspartyl residues in age-damaged proteins as part of an, essential protein repair process. Here, we report crystal structures of, the repair methyltransferase at resolutions up to 1.2 A from the, hyperthermophilic archaeon Pyrococcus furiosus. Refined structures include, binary complexes with the active cofactor AdoMet, its reaction product, S-adenosylhomocysteine (AdoHcy), and adenosine. The enzyme places the, methyl-donating cofactor in a deep, electrostatically negative pocket that, is shielded from solvent. Across the multiple crystal structures, visualized, the presence or absence of the methyl group on the cofactor, correlates with a significant conformational change in the enzyme in a, loop bordering the active site, suggesting a role for motion in catalysis, or cofactor exchange. We also report the structure of a ternary complex of, the enzyme with adenosine and the methyl-accepting polypeptide substrate, VYP(L-isoAsp)HA at 2.1 A. The substrate binds in a narrow active site, cleft with three of its residues in an extended conformation, suggesting, that damaged proteins may be locally denatured during the repair process, in cells. Manual and computer-based docking studies on different isomers, help explain how the enzyme uses steric effects to make the critical, distinction between normal L-aspartyl and age-damaged L-isoaspartyl and, D-aspartyl residues.
<StructureSection load='1jg3' size='340' side='right'caption='[[1jg3]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1jg3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JG3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JG3 FirstGlance]. <br>
1JG3 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus] with CL, NA and ADN 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=1JG3 OCA].  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IAS:BETA-L-ASPARTIC+ACID'>IAS</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1jg3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jg3 OCA], [https://pdbe.org/1jg3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jg3 RCSB], [https://www.ebi.ac.uk/pdbsum/1jg3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jg3 ProSAT]</span></td></tr>
Crystal structure of a protein repair methyltransferase from Pyrococcus furiosus with its L-isoaspartyl peptide substrate., Griffith SC, Sawaya MR, Boutz DR, Thapar N, Katz JE, Clarke S, Yeates TO, J Mol Biol. 2001 Nov 9;313(5):1103-16. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11700066 11700066]
</table>
[[Category: Protein-L-isoaspartate(D-aspartate) O-methyltransferase]]
== Function ==
[https://www.uniprot.org/uniprot/PIMT_PYRFU PIMT_PYRFU] 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 (By similarity).
== 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/jg/1jg3_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=1jg3 ConSurf].
<div style="clear:both"></div>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pyrococcus furiosus]]
[[Category: Pyrococcus furiosus]]
[[Category: Single protein]]
[[Category: Boutz D]]
[[Category: Boutz, D.]]
[[Category: Clarke S]]
[[Category: Clarke, S.]]
[[Category: Griffith SC]]
[[Category: Griffith, S.C.]]
[[Category: Katz J]]
[[Category: Katz, J.]]
[[Category: Sawaya MR]]
[[Category: Sawaya, M.R.]]
[[Category: Thapar N]]
[[Category: Thapar, N.]]
[[Category: Yeates TO]]
[[Category: Yeates, T.O.]]
[[Category: ADN]]
[[Category: CL]]
[[Category: NA]]
[[Category: protein repair isomerization]]
[[Category: rossmann methyltransferase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 18:12:56 2007''

Latest revision as of 10:52, 3 April 2024

Crystal Structure of L-isoaspartyl (D-aspartyl) O-methyltransferase with adenosine & VYP(ISP)HA substrateCrystal Structure of L-isoaspartyl (D-aspartyl) O-methyltransferase with adenosine & VYP(ISP)HA substrate

Structural highlights

1jg3 is a 4 chain structure with sequence from Pyrococcus furiosus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.1Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PIMT_PYRFU 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 (By similarity).

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

1jg3, resolution 2.10Å

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OCA
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