1n2x: Difference between revisions

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<StructureSection load='1n2x' size='340' side='right'caption='[[1n2x]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='1n2x' size='340' side='right'caption='[[1n2x]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1n2x]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N2X OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1N2X FirstGlance]. <br>
<table><tr><td colspan='2'>[[1n2x]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N2X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N2X FirstGlance]. <br>
</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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.9&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1m6y|1m6y]]</div></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=1n2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n2x OCA], [https://pdbe.org/1n2x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n2x RCSB], [https://www.ebi.ac.uk/pdbsum/1n2x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n2x ProSAT], [https://www.topsan.org/Proteins/MCSG/1n2x TOPSAN]</span></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TM0872 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1n2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n2x OCA], [http://pdbe.org/1n2x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n2x RCSB], [http://www.ebi.ac.uk/pdbsum/1n2x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1n2x ProSAT], [http://www.topsan.org/Proteins/MCSG/1n2x TOPSAN]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/RSMH_THEMA RSMH_THEMA]] Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA.[HAMAP-Rule:MF_01007]  
[https://www.uniprot.org/uniprot/RSMH_THEMA RSMH_THEMA] Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA.[HAMAP-Rule:MF_01007]
== 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=1n2x 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=1n2x ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
S-adenosyl-L-methionine-dependent methyltransferases (MTs) are abundant, and highly conserved across phylogeny. These enzymes use the cofactor AdoMet to methylate a wide variety of molecular targets, thereby modulating important cellular and metabolic activities. Thermotoga maritima protein 0872 (TM0872) belongs to a large sequence family of predicted MTs, ranging phylogenetically from relatively simple bacteria to humans. The genes for many of the bacterial homologs are located within operons involved in cell wall synthesis and cell division. Despite preliminary biochemical studies in E. coli and B. subtilis, the substrate specificity of this group of more than 150 proteins is unknown. As part of the Midwest Center for Structural Genomics initiative (www.mcsg.anl.gov), we have determined the structure of TM0872 in complexes with AdoMet and with S-adenosyl-L-homocysteine (AdoHcy). As predicted, TM0872 has a typical MT domain, and binds endogenous AdoMet, or co-crystallized AdoHcy, in a manner consistent with other known MT structures. In addition, TM0872 has a second domain that is novel among MTs in both its location in the sequence and its structure. The second domain likely acts in substrate recognition and binding, and there is a potential substrate-binding cleft spanning the two domains. This long and narrow cleft is lined with positively charged residues which are located opposite the S(+)-CH(3) bond, suggesting that a negatively charged molecule might be targeted for catalysis. However, AdoMet and AdoHcy are both buried, and access to the methyl group would presumably require structural rearrangement. These TM0872 crystal structures offer the first structural glimpses at this phylogenetically conserved sequence family.
Crystal complexes of a predicted S-adenosylmethionine-dependent methyltransferase reveal a typical AdoMet binding domain and a substrate recognition domain.,Miller DJ, Ouellette N, Evdokimova E, Savchenko A, Edwards A, Anderson WF Protein Sci. 2003 Jul;12(7):1432-42. PMID:12824489<ref>PMID:12824489</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1n2x" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 43589]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Anderson, W F]]
[[Category: Thermotoga maritima]]
[[Category: Structural genomic]]
[[Category: Anderson WF]]
[[Category: Miller, D J]]
[[Category: Miller DJ]]
[[Category: Mcsg]]
[[Category: PSI, Protein structure initiative]]
[[Category: Protein-sam methyl donor complex]]
[[Category: Sam-dependent methyltransferase fold]]
[[Category: Transferase]]

Revision as of 11:45, 10 April 2024

Crystal Structure Analysis of TM0872, a Putative SAM-dependent Methyltransferase, Complexed with SAMCrystal Structure Analysis of TM0872, a Putative SAM-dependent Methyltransferase, Complexed with SAM

Structural highlights

1n2x is a 2 chain structure with sequence from Thermotoga maritima. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.9Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

RSMH_THEMA Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA.[HAMAP-Rule:MF_01007]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

1n2x, resolution 1.90Å

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OCA
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