1jg2: Difference between revisions

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==Crystal Structure of L-isoaspartyl (D-aspartyl) O-methyltransferase with adenosine==
The line below this paragraph, containing "STRUCTURE_1jg2", creates the "Structure Box" on the page.
<StructureSection load='1jg2' size='340' side='right'caption='[[1jg2]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1jg2]] is a 1 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=1JG2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JG2 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#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=ADN:ADENOSINE'>ADN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
{{STRUCTURE_1jg2|  PDB=1jg2  |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1jg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jg2 OCA], [https://pdbe.org/1jg2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jg2 RCSB], [https://www.ebi.ac.uk/pdbsum/1jg2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jg2 ProSAT]</span></td></tr>
 
</table>
'''Crystal Structure of L-isoaspartyl (D-aspartyl) O-methyltransferase with adenosine'''
== 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 ==
==Overview==
[[Image:Consurf_key_small.gif|200px|right]]
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.
Check<jmol>
 
  <jmolCheckbox>
==About this Structure==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jg/1jg2_consurf.spt"</scriptWhenChecked>
1JG2 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JG2 OCA].  
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==Reference==
  </jmolCheckbox>
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://www.ncbi.nlm.nih.gov/pubmed/11700066 11700066]
</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=1jg2 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: Protein repair isomerization]]
[[Category: Rossman methyltransferase]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 21:10:52 2008''

Latest revision as of 10:39, 7 February 2024

Crystal Structure of L-isoaspartyl (D-aspartyl) O-methyltransferase with adenosineCrystal Structure of L-isoaspartyl (D-aspartyl) O-methyltransferase with adenosine

Structural highlights

1jg2 is a 1 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 1.5Å
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.

1jg2, resolution 1.50Å

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OCA
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