1rg9: Difference between revisions

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-[[Image:1rg9.gif|left|200px]]<br /><applet load="1rg9" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1rg9, resolution 2.5&Aring;" />
-'''S-Adenosylmethionine synthetase complexed with SAM and PPNP'''<br />
-==Overview==
+==S-Adenosylmethionine synthetase complexed with SAM and PPNP==
-S-Adenosylmethionine synthetase (MAT) catalyzes formation of, S-adenosylmethionine (SAM) from ATP and l-methionine (Met) and hydrolysis, of tripolyphosphate to PP(i) and P(i). Escherichia coli MAT (eMAT) has, been crystallized with the ATP analogue AMPPNP and Met, and the crystal, structure has been determined at 2.5 A resolution. eMAT is a dimer of, dimers and has a 222 symmetry. Each active site contains the products SAM, and PPNP. A modeling study indicates that the substrates (AMPPNP and Met), can bind at the same sites as the products, and only a small conformation, change of the ribose ring is needed for conversion of the substrates to, the products. On the basis of the ternary complex structure and a modeling, study, a novel catalytic mechanism of SAM formation is proposed. In the, mechanism, neutral His14 acts as an acid to cleave the C5'-O5' bond of ATP, while simultaneously a change in the ribose ring conformation from C4'-exo, to C3'-endo occurs, and the S of Met makes a nucleophilic attack on the, C5' to form SAM. All essential amino acid residues for substrate binding, found in eMAT are conserved in the rat liver enzyme, indicating that the, bacterial and mammalian enzymes have the same catalytic mechanism., However, a catalytic mechanism proposed recently by Gonzalez et al. based, on the structures of three ternary complexes of rat liver MAT [Gonzalez, B., Pajares, M. A., Hermoso, J. A., Guillerm, D., Guillerm, G., and, Sanz-Aparicio. J. (2003) J. Mol. Biol. 331, 407] is substantially, different from our mechanism.
+<StructureSection load='1rg9' size='340' side='right'caption='[[1rg9]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1rg9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RG9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RG9 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]] 2.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PPK:(DIPHOSPHONO)AMINOPHOSPHONIC+ACID'>PPK</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</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=1rg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rg9 OCA], [https://pdbe.org/1rg9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rg9 RCSB], [https://www.ebi.ac.uk/pdbsum/1rg9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rg9 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/METK_ECOLI METK_ECOLI] Catalyzes the formation of S-adenosylmethionine from methionine and ATP. The overall synthetic reaction is composed of two sequential steps, AdoMet formation and the subsequent tripolyphosphate hydrolysis which occurs prior to release of AdoMet from the enzyme. Is essential for growth.[HAMAP-Rule:MF_00086]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rg/1rg9_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1rg9 ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-RG9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with K, MG, SAM and PPK as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Methionine_adenosyltransferase Methionine adenosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.6 2.5.1.6] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1RG9 OCA].
+*[[S-adenosylmethionine synthetase 3D structures|S-adenosylmethionine synthetase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Crystal structure of the S-adenosylmethionine synthetase ternary complex: a novel catalytic mechanism of S-adenosylmethionine synthesis from ATP and Met., Komoto J, Yamada T, Takata Y, Markham GD, Takusagawa F, Biochemistry. 2004 Feb 24;43(7):1821-31. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14967023 14967023]
 [[Category: Escherichia coli]]
-[[Category: Methionine adenosyltransferase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Komoto J]]
-[[Category: Komoto, J.]]
+[[Category: Markham GD]]
-[[Category: Markham, G.D.]]
+[[Category: Takata Y]]
-[[Category: Takata, Y.]]
+[[Category: Takusagawa F]]
-[[Category: Takusagawa, F.]]
+[[Category: Yamada T]]
-[[Category: Yamada, T.]]
-[[Category: K]]
-[[Category: MG]]
-[[Category: PPK]]
-[[Category: SAM]]
-[[Category: s-adenosylmethionine synthetase; methionine adenosyltransferase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 01:34:14 2007''