5h5d

From Proteopedia

(Difference between revisions)

Current revision

The crystal structure of the yeast arginine methyltransferase SFM1 complexed with MTA

Structural highlights

5h5d is a 1 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.7Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SFM1_YEAST S-adenosyl-L-methionine-dependent protein-arginine N-methyltransferase that monomethylates ribosomal protein S3 (RPS3) at 'Arg-146'.^[1]

Publication Abstract from PubMed

Arginine methylation is a common post-translational modification and is critical for many cellular processes. Sfm1 is a novel arginine methyltransferase that contains a SpoU-TrmD (SPOUT) domain, a typical fold known for RNA methylation, but acts on a ribosomal protein. The underlying mechanism is poorly understood. Here, we report cocrystal structures of Sfm1 in complex with various ligands. We found that a critical loop responsible for S-adenosyl-l-methionine (SAM) binding adopts a different conformation from previous reports, and SAM appears to exhibit double conformations. Deletion of this loop greatly reduces the affinity of Sfm1 to SAM. Additionally, by comparison to closely related tRNA-methyltransferase Trm10, our structural analyses offer a good explanation why the two enzymes utilize distinct substrates, providing insights into the molecular mechanism.

A flexible cofactor-binding loop in the novel arginine methyltransferase Sfm1.,Wang C, Zeng J, Xie W FEBS Lett. 2016 Dec 19. doi: 10.1002/1873-3468.12533. PMID:27990635^[2]

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

References

↑ Young BD, Weiss DI, Zurita-Lopez CI, Webb KJ, Clarke SG, McBride AE. Identification of methylated proteins in the yeast small ribosomal subunit: a role for SPOUT methyltransferases in protein arginine methylation. Biochemistry. 2012 Jun 26;51(25):5091-104. doi: 10.1021/bi300186g. Epub 2012 Jun , 15. PMID:22650761 doi:http://dx.doi.org/10.1021/bi300186g
↑ Wang C, Zeng J, Xie W. A flexible cofactor-binding loop in the novel arginine methyltransferase Sfm1. FEBS Lett. 2016 Dec 19. doi: 10.1002/1873-3468.12533. PMID:27990635 doi:http://dx.doi.org/10.1002/1873-3468.12533

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5h5d"

Categories: Large Structures | Saccharomyces cerevisiae S288C | Wang C | Xie W | Zeng J

@@ Line 1: / Line 1: @@
 ==The crystal structure of the yeast arginine methyltransferase SFM1 complexed with MTA==
-<StructureSection load='5h5d' size='340' side='right' caption='[[5h5d]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+<StructureSection load='5h5d' size='340' side='right'caption='[[5h5d]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5h5d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H5D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H5D FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5h5d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H5D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5H5D FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5h5f|5h5f]], [[5h5e|5h5e]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene></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=5h5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h5d OCA], [http://pdbe.org/5h5d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h5d RCSB], [http://www.ebi.ac.uk/pdbsum/5h5d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h5d 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=5h5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h5d OCA], [https://pdbe.org/5h5d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5h5d RCSB], [https://www.ebi.ac.uk/pdbsum/5h5d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5h5d ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SFM1_YEAST SFM1_YEAST]] S-adenosyl-L-methionine-dependent protein-arginine N-methyltransferase that monomethylates ribosomal protein S3 (RPS3) at 'Arg-146'.<ref>PMID:22650761</ref>
+[https://www.uniprot.org/uniprot/SFM1_YEAST SFM1_YEAST] S-adenosyl-L-methionine-dependent protein-arginine N-methyltransferase that monomethylates ribosomal protein S3 (RPS3) at 'Arg-146'.<ref>PMID:22650761</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Wang, C]]
+[[Category: Large Structures]]
-[[Category: Xie, W]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Zeng, J]]
+[[Category: Wang C]]
-[[Category: Arginine methyltransferase]]
+[[Category: Xie W]]
-[[Category: Spout fold]]
+[[Category: Zeng J]]
-[[Category: Transferase]]

5h5d

From Proteopedia

Current revision

The crystal structure of the yeast arginine methyltransferase SFM1 complexed with MTA

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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