This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1jg4

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:39, 7 February 2024) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1jg4.jpg|left|200px]]<br /><applet load="1jg4" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1jg4, resolution 1.5&Aring;" />
 
-
'''Crystal Structure of L-isoaspartyl (D-aspartyl) O-methyltransferase with S-adenosylmethionine'''<br />
 
-
==Overview==
+
==Crystal Structure of L-isoaspartyl (D-aspartyl) O-methyltransferase with S-adenosylmethionine==
-
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='1jg4' size='340' side='right'caption='[[1jg4]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[1jg4]] 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=1JG4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JG4 FirstGlance]. <br>
-
1JG4 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 <scene name='pdbligand=SAM:'>SAM</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1JG4 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]] 1.5&#8491;</td></tr>
-
 
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</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=1jg4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jg4 OCA], [https://pdbe.org/1jg4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jg4 RCSB], [https://www.ebi.ac.uk/pdbsum/1jg4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jg4 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/1jg4_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=1jg4 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: SAM]]
+
-
[[Category: protein repair isomerization]]
+
-
[[Category: rossmann methyltransferase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:22:17 2008''
+

Current revision

Crystal Structure of L-isoaspartyl (D-aspartyl) O-methyltransferase with S-adenosylmethionine

PDB ID 1jg4

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1jg4"
Personal tools