5f8f: Difference between revisions

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~~'''Unreleased structure'''~~

The ~~entry 5f8f~~ is ~~ON HOLD~~

==Rv2258c-SFG==

== Structural highlights ==

<table><tr><td colspan='2'>[[5f8f]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5F8F FirstGlance]. <br>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SFG:SINEFUNGIN'>SFG</scene></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=5f8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f8f OCA], [https://pdbe.org/5f8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5f8f RCSB], [https://www.ebi.ac.uk/pdbsum/5f8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5f8f ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/Y2258_MYCTU Y2258_MYCTU] Probable methyltransferase that may target bulky nonpolar molecules with aromatic rings.<ref>PMID:26772148</ref>

== Publication Abstract from PubMed ==

The Mycobacterium tuberculosis Rv2258c protein is an S-adenosyl-L-methionine (SAM)-dependent methyltransferase (MTase). Here, we have determined its crystal structure in three forms: a ligand-unbound form, a binary complex with sinefungin (SFG), and a binary complex with S-adenosyl-L-homocysteine (SAH). The monomer structure of Rv2258c consists of two domains which are linked by a long alpha-helix. The N-terminal domain is essential for dimerization and the C-terminal domain has the Class I MTase fold. Rv2258c forms a homodimer in the crystal, with the N-terminal domains facing each other. It also exists as a homodimer in solution. A DALI structural similarity search with Rv2258c reveals that the overall structure of Rv2258c is very similar to small-molecule SAM-dependent MTases. Rv2258c interacts with the bound SFG (or SAH) in an extended conformation maintained by a network of hydrogen bonds and stacking interactions. Rv2258c has a relatively large hydrophobic cavity for binding of the methyl-accepting substrate, suggesting that bulky nonpolar molecules with aromatic rings might be targeted for methylation by Rv2258c in M. tuberculosis. However, the ligand-binding specificity and the biological role of Rv2258c remain to be elucidated due to high variability of the amino acid residues defining the substrate-binding site.

~~Authors:~~ Im, ~~Ha Na~~, Suh, ~~Se Won~~

Crystal structure of Rv2258c from Mycobacterium tuberculosis H37Rv, an S-adenosyl-l-methionine-dependent methyltransferase.,Im HN, Kim HS, An DR, Jang JY, Kim J, Yoon HJ, Yang JK, Suh SW J Struct Biol. 2016 Mar;193(3):172-80. doi: 10.1016/j.jsb.2016.01.002. Epub 2016 , Jan 6. PMID:26772148<ref>PMID:26772148</ref>

~~Description~~: ~~Rv2258c-unbound~~

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

[[Category: ~~Unreleased~~ Structures]]

</div>

[[Category: Im~~, Ha Na,~~ Suh~~, Se Won~~]]

== References ==

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Mycobacterium tuberculosis H37Rv]]

[[Category: Im HN]]

[[Category: Suh SW]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5f8f is ON HOLD
+==Rv2258c-SFG==
+<StructureSection load='5f8f' size='340' side='right'caption='[[5f8f]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5f8f]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5F8F FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SFG:SINEFUNGIN'>SFG</scene></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=5f8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f8f OCA], [https://pdbe.org/5f8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5f8f RCSB], [https://www.ebi.ac.uk/pdbsum/5f8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5f8f ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Y2258_MYCTU Y2258_MYCTU] Probable methyltransferase that may target bulky nonpolar molecules with aromatic rings.<ref>PMID:26772148</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The Mycobacterium tuberculosis Rv2258c protein is an S-adenosyl-L-methionine (SAM)-dependent methyltransferase (MTase). Here, we have determined its crystal structure in three forms: a ligand-unbound form, a binary complex with sinefungin (SFG), and a binary complex with S-adenosyl-L-homocysteine (SAH). The monomer structure of Rv2258c consists of two domains which are linked by a long alpha-helix. The N-terminal domain is essential for dimerization and the C-terminal domain has the Class I MTase fold. Rv2258c forms a homodimer in the crystal, with the N-terminal domains facing each other. It also exists as a homodimer in solution. A DALI structural similarity search with Rv2258c reveals that the overall structure of Rv2258c is very similar to small-molecule SAM-dependent MTases. Rv2258c interacts with the bound SFG (or SAH) in an extended conformation maintained by a network of hydrogen bonds and stacking interactions. Rv2258c has a relatively large hydrophobic cavity for binding of the methyl-accepting substrate, suggesting that bulky nonpolar molecules with aromatic rings might be targeted for methylation by Rv2258c in M. tuberculosis. However, the ligand-binding specificity and the biological role of Rv2258c remain to be elucidated due to high variability of the amino acid residues defining the substrate-binding site.
-Authors: Im, Ha Na, Suh, Se Won
+Crystal structure of Rv2258c from Mycobacterium tuberculosis H37Rv, an S-adenosyl-l-methionine-dependent methyltransferase.,Im HN, Kim HS, An DR, Jang JY, Kim J, Yoon HJ, Yang JK, Suh SW J Struct Biol. 2016 Mar;193(3):172-80. doi: 10.1016/j.jsb.2016.01.002. Epub 2016 , Jan 6. PMID:26772148<ref>PMID:26772148</ref>
-Description: Rv2258c-unbound
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Im, Ha Na, Suh, Se Won]]
+<div class="pdbe-citations 5f8f" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Mycobacterium tuberculosis H37Rv]]
+[[Category: Im HN]]
+[[Category: Suh SW]]