1v9a: Difference between revisions

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OCA

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-[[Image:1v9a.gif|left|200px]]<br /><applet load="1v9a" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1v9a, resolution 2.00&Aring;" />
-'''Crystal structure of Uroporphyrin-III C-methyl transferase from Thermus thermophilus complexed with S-adenyl homocysteine'''<br />
-==Overview==
+==Crystal structure of Uroporphyrin-III C-methyl transferase from Thermus thermophilus complexed with S-adenyl homocysteine==
-Uroporphyrinogen-III C-methyltransferase from Thermus thermophilus is a, multifunctional protein responsible for two of the eight, S-adenosyl-methionine-dependent methylations of the corrin ring during, vitamin B(12) synthesis. The structure of this protein has been solved to, 2.0 A resolution in both the apo and cofactor-bound form. The monomer, consists of two domains, A and B, each consisting of a five-stranded, beta-sheet and two or three alpha-helices, with the cofactor bound at the, interface. The biological unit is the dimer found in the asymmetric unit., This dimer is related by a non-crystallographic twofold such that two B, domains combine to form a long ten-stranded beta-sheet. When compared with, solved related structures, this structure shows clear differences in the, region involved in cofactor and substrate binding, affirming the role of, several previously implicated residues and questioning others. The solved, related structures are characterized by an exposed active site. The T., thermophilus structure has this site restricted by the interaction of a, flexible loop structure with a highly conserved residue, suggesting a, mechanistic role. This structure represents the ;closed' form of the, protein.
+<StructureSection load='1v9a' size='340' side='right'caption='[[1v9a]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1v9a]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V9A 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&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</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=1v9a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9a OCA], [https://pdbe.org/1v9a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v9a RCSB], [https://www.ebi.ac.uk/pdbsum/1v9a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v9a ProSAT], [https://www.topsan.org/Proteins/RSGI/1v9a TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q5SKH6_THET8 Q5SKH6_THET8]
+== 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/v9/1v9a_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=1v9a ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Uroporphyrinogen-III C-methyltransferase from Thermus thermophilus is a multifunctional protein responsible for two of the eight S-adenosyl-methionine-dependent methylations of the corrin ring during vitamin B(12) synthesis. The structure of this protein has been solved to 2.0 A resolution in both the apo and cofactor-bound form. The monomer consists of two domains, A and B, each consisting of a five-stranded beta-sheet and two or three alpha-helices, with the cofactor bound at the interface. The biological unit is the dimer found in the asymmetric unit. This dimer is related by a non-crystallographic twofold such that two B domains combine to form a long ten-stranded beta-sheet. When compared with solved related structures, this structure shows clear differences in the region involved in cofactor and substrate binding, affirming the role of several previously implicated residues and questioning others. The solved related structures are characterized by an exposed active site. The T. thermophilus structure has this site restricted by the interaction of a flexible loop structure with a highly conserved residue, suggesting a mechanistic role. This structure represents the ;closed' form of the protein.
-==About this Structure==
+Structure of a closed-form uroporphyrinogen-III C-methyltransferase from Thermus thermophilus.,Rehse PH, Kitao T, Tahirov TH Acta Crystallogr D Biol Crystallogr. 2005 Jul;61(Pt 7):913-9. Epub 2005, Jun 24. PMID:15983414<ref>PMID:15983414</ref>
-V9A is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with FLC and SAH as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Uroporphyrinogen-III_C-methyltransferase Uroporphyrinogen-III C-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.107 2.1.1.107] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1V9A OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structure of a closed-form uroporphyrinogen-III C-methyltransferase from Thermus thermophilus., Rehse PH, Kitao T, Tahirov TH, Acta Crystallogr D Biol Crystallogr. 2005 Jul;61(Pt 7):913-9. Epub 2005, Jun 24. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15983414 15983414]
+</div>
-[[Category: Single protein]]
+<div class="pdbe-citations 1v9a" style="background-color:#fffaf0;"></div>
-[[Category: Thermus thermophilus]]
+== References ==
-[[Category: Uroporphyrinogen-III C-methyltransferase]]
+<references/>
-[[Category: Kitao, T.]]
+__TOC__
-[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
+</StructureSection>
-[[Category: Rehse, P.H.]]
+[[Category: Large Structures]]
-[[Category: Tahirov, T.H.]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: FLC]]
+[[Category: Kitao T]]
-[[Category: SAH]]
+[[Category: Rehse PH]]
-[[Category: riken structural genomics/proteomics initiative]]
+[[Category: Tahirov TH]]
-[[Category: rsgi]]
-[[Category: structural genomics]]
-[[Category: transferase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 21:54:11 2007''