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==X-ray Structure of a C-3'-Methyltransferase in Complex with S-Adenosyl-L-Homocysteine and Sugar Product==
==X-ray Structure of a C-3'-Methyltransferase in Complex with S-Adenosyl-L-Homocysteine and Sugar Product==
<StructureSection load='3ndj' size='340' side='right' caption='[[3ndj]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
<StructureSection load='3ndj' size='340' side='right'caption='[[3ndj]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3ndj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micromonospora_chalcease"_(sic)_(foulerton_1905)_orskov_1923 "micromonospora chalcease" (sic) (foulerton 1905) orskov 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NDJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NDJ FirstGlance]. <br>
<table><tr><td colspan='2'>[[3ndj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Micromonospora_chalcea Micromonospora chalcea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NDJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NDJ FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=JHZ:(2R,4S,6R)-4-amino-4,6-dimethyl-5-oxotetrahydro-2H-pyran-2-yl+[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl+dihydrogen+diphosphate+(non-preferred+name)'>JHZ</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.5&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ndi|3ndi]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=JHZ:(2R,4S,6R)-4-amino-4,6-dimethyl-5-oxotetrahydro-2H-pyran-2-yl+[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl+dihydrogen+diphosphate+(non-preferred+name)'>JHZ</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">tcab9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1874 "Micromonospora chalcease" (sic) (Foulerton 1905) Orskov 1923])</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=3ndj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ndj OCA], [https://pdbe.org/3ndj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ndj RCSB], [https://www.ebi.ac.uk/pdbsum/3ndj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ndj ProSAT]</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=3ndj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ndj OCA], [http://pdbe.org/3ndj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ndj RCSB], [http://www.ebi.ac.uk/pdbsum/3ndj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ndj ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/B5L6K6_MICCH B5L6K6_MICCH]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=3ndj ConSurf].
</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=3ndj ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
S-Adenosylmethionine (SAM)-dependent methyltransferases are involved in a myriad of biological processes, including signal transduction, chromatin repair, metabolism, and biosyntheses, among others. Here we report the high-resolution structure of a novel C-3'-methyltransferase involved in the production of d-tetronitrose, an unusual sugar found attached to the antitumor agent tetrocarcin A or the antibiotic kijanimicin. Specifically, this enzyme, referred to as TcaB9 and cloned from Micromonospora chalcea, catalyzes the conversion of dTDP-3-amino-2,3,6-trideoxy-4-keto-d-glucose to dTDP-3-amino-2,3,6-trideoxy-4-keto-3-methyl-d-glucose. For this analysis, two structures were determined to 1.5 A resolution: one in which the enzyme was crystallized in the presence of SAM and dTMP and the other with the protein complexed to S-adenosylhomocysteine and its dTDP-linked sugar product. The overall fold of the monomeric enzyme can be described in terms of three domains. The N-terminal domain harbors the binding site for a zinc ion that is ligated by four cysteines. The middle domain adopts the canonical "SAM-binding" fold with a seven-stranded mixed beta-sheet flanked on either side by three alpha-helices. This domain is responsible for anchoring the SAM cofactor to the protein. Strikingly, the C-terminal domain also contains a seven-stranded beta-sheet, and it appears to be related to the middle domain by an approximate 2-fold rotational axis, thus suggesting TcaB9 arose via gene duplication. Key residues involved in sugar binding include His 181, Glu 224, His 225, and Tyr 222. Their possible roles in catalysis are discussed.
Molecular Architecture of a C-3'-Methyltransferase Involved in the Biosynthesis of d-Tetronitrose.,Bruender NA, Thoden JB, Kaur M, Avey MK, Holden HM Biochemistry. 2010 Jun 22. PMID:20527922<ref>PMID:20527922</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3ndj" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Avey, M K]]
[[Category: Large Structures]]
[[Category: Bruender, N A]]
[[Category: Holden, H M]]
[[Category: Kaur, M]]
[[Category: Thoden, J B]]
[[Category: C-3'-methyltransferase]]
[[Category: Keto sugar]]
[[Category: Kijanose]]
[[Category: Micromonospora chalcea]]
[[Category: Micromonospora chalcea]]
[[Category: S-adenosyl-l-homocysteine]]
[[Category: Avey MK]]
[[Category: Sugar methylation]]
[[Category: Bruender NA]]
[[Category: Tcab9]]
[[Category: Holden HM]]
[[Category: Tetradeoxy sugar]]
[[Category: Kaur M]]
[[Category: Tetronitrose]]
[[Category: Thoden JB]]
[[Category: Transferase]]

Latest revision as of 10:29, 21 February 2024

X-ray Structure of a C-3'-Methyltransferase in Complex with S-Adenosyl-L-Homocysteine and Sugar Product

3ndj, resolution 1.50Å

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