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1p0y

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Revision as of 09:23, 8 September 2021

Crystal structure of the SET domain of LSMT bound to MeLysine and AdoHcy

Structural highlights

1p0y is a 3 chain structure with sequence from Garden pea. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	1mlv, 1ozv
Activity:	[Ribulose-bisphosphate_carboxylase-lysine_N-methyltransferase [Ribulose-bisphosphate carboxylase]-lysine N-methyltransferase], with EC number 2.1.1.127
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RBCMT_PEA] Methylates 'Lys-14' of the large subunit of RuBisCO. Can also use with lower efficiency chloroplastic fructose-bisphosphate aldolases and gamma-tocopherol methyltransferase as substrates, but not a cytosolic aldolase.^[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 PubMed

SET domain protein methyltransferases catalyze the transfer of methyl groups from the cofactor S-adenosylmethionine (AdoMet) to specific lysine residues of protein substrates, such as the N-terminal tails of histones H3 and H4 and the large subunit of the Rubisco holoenzyme complex. The crystal structures of pea Rubisco large subunit methyltransferase (LSMT) in ternary complexes with either lysine or epsilon-N-methyllysine (MeLys) and the product S-adenosylhomocysteine (AdoHcy) were determined to resolutions of 2.65 and 2.55 A, respectively. The zeta-methyl group of MeLys is bound to the enzyme via carbon-oxygen hydrogen bonds that play a key role in catalysis. The methyl donor and acceptor are aligned in a linear geometry for S(N)2 nucleophilic transfer of the methyl group during catalysis. Differences in hydrogen bonding between the MeLys epsilon-amino group and Rubisco LSMT and SET7/9 explain why Rubisco LSMT generates multiply methylated Lys, wheras SET7/9 generates only MeLys.

Mechanism of multiple lysine methylation by the SET domain enzyme Rubisco LSMT.,Trievel RC, Flynn EM, Houtz RL, Hurley JH Nat Struct Biol. 2003 Jul;10(7):545-52. PMID:12819771^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Mininno M, Brugiere S, Pautre V, Gilgen A, Ma S, Ferro M, Tardif M, Alban C, Ravanel S. Characterization of chloroplastic fructose 1,6-bisphosphate aldolases as lysine-methylated proteins in plants. J Biol Chem. 2012 Jun 15;287(25):21034-44. doi: 10.1074/jbc.M112.359976. Epub, 2012 Apr 30. PMID:22547063 doi:http://dx.doi.org/10.1074/jbc.M112.359976
↑ Trievel RC, Flynn EM, Houtz RL, Hurley JH. Mechanism of multiple lysine methylation by the SET domain enzyme Rubisco LSMT. Nat Struct Biol. 2003 Jul;10(7):545-52. PMID:12819771 doi:http://dx.doi.org/10.1038/nsb946

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1p0y"

@@ Line 3: / Line 3: @@
 <StructureSection load='1p0y' size='340' side='right'caption='[[1p0y]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1p0y]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Garden_pea Garden pea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P0Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P0Y FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1p0y]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Garden_pea Garden pea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P0Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P0Y FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLZ:N-METHYL-LYSINE'>MLZ</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLZ:N-METHYL-LYSINE'>MLZ</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1mlv|1mlv]], [[1ozv|1ozv]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1mlv|1mlv]], [[1ozv|1ozv]]</div></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Ribulose-bisphosphate_carboxylase]-lysine_N-methyltransferase [Ribulose-bisphosphate carboxylase]-lysine N-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.127 2.1.1.127] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/[Ribulose-bisphosphate_carboxylase]-lysine_N-methyltransferase [Ribulose-bisphosphate carboxylase]-lysine N-methyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.127 2.1.1.127] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1p0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p0y OCA], [http://pdbe.org/1p0y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1p0y RCSB], [http://www.ebi.ac.uk/pdbsum/1p0y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1p0y ProSAT]</span></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=1p0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p0y OCA], [https://pdbe.org/1p0y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p0y RCSB], [https://www.ebi.ac.uk/pdbsum/1p0y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p0y ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RBCMT_PEA RBCMT_PEA]] Methylates 'Lys-14' of the large subunit of RuBisCO. Can also use with lower efficiency chloroplastic fructose-bisphosphate aldolases and gamma-tocopherol methyltransferase as substrates, but not a cytosolic aldolase.<ref>PMID:22547063</ref>
+[[https://www.uniprot.org/uniprot/RBCMT_PEA RBCMT_PEA]] Methylates 'Lys-14' of the large subunit of RuBisCO. Can also use with lower efficiency chloroplastic fructose-bisphosphate aldolases and gamma-tocopherol methyltransferase as substrates, but not a cytosolic aldolase.<ref>PMID:22547063</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 32: @@
 ==See Also==
-*[[RuBisCO|RuBisCO]]
+*[[RuBisCO 3D structures|RuBisCO 3D structures]]
 == References ==
 <references/>

1p0y

From Proteopedia

Revision as of 09:23, 8 September 2021

Crystal structure of the SET domain of LSMT bound to MeLysine and AdoHcy

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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