3llf: Difference between revisions

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-{{Seed}}
-[[Image:3llf.jpg|left|200px]]
-<!--
+==Crystal structure of the mutant S127P of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 6-azauridine 5'-monophosphate==
-The line below this paragraph, containing "STRUCTURE_3llf", creates the "Structure Box" on the page.
+<StructureSection load='3llf' size='340' side='right'caption='[[3llf]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3llf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus_str._Delta_H Methanothermobacter thermautotrophicus str. Delta H]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LLF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LLF FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UP6:6-AZA+URIDINE+5-MONOPHOSPHATE'>UP6</scene></td></tr>
-{{STRUCTURE_3llf|  PDB=3llf  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3llf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3llf OCA], [https://pdbe.org/3llf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3llf RCSB], [https://www.ebi.ac.uk/pdbsum/3llf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3llf ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PYRF_METTH PYRF_METTH] Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_A]
+== 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/ll/3llf_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=3llf ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structural factors responsible for the extraordinary rate enhancement ( approximately 10(17)) of the reaction catalyzed by orotidine 5'-monophosphate decarboxylase (OMPDC) have not been defined. Catalysis requires a conformational change that closes an active site loop and "clamps" the orotate base proximal to hydrogen-bonded networks that destabilize the substrate and stabilize the intermediate. In the OMPDC from Methanobacter thermoautotrophicus, a "remote" structurally conserved cluster of hydrophobic residues that includes Val 182 in the active site loop is assembled in the closed, catalytically active conformation. Substitution of these residues with Ala decreases k(cat)/K(m) with a minimal effect on k(cat), providing evidence that the cluster stabilizes the closed conformation. The intrinsic binding energies of the 5'-phosphate group of orotidine 5'-monophosphate for the mutant enzymes are similar to that for the wild type, supporting this conclusion.
-===Crystal structure of the mutant S127P of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 6-azauridine 5'-monophosphate===
+Conformational changes in orotidine 5'-monophosphate decarboxylase: "remote" residues that stabilize the active conformation.,Wood BM, Amyes TL, Fedorov AA, Fedorov EV, Shabila A, Almo SC, Richard JP, Gerlt JA Biochemistry. 2010 May 4;49(17):3514-6. PMID:20369850<ref>PMID:20369850</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3llf" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20369850}}, adds the Publication Abstract to the page
+*[[Uridine 5'-monophosphate synthase 3D structures|Uridine 5'-monophosphate synthase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20369850 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20369850}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-LLF is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LLF OCA].
+[[Category: Methanothermobacter thermautotrophicus str. Delta H]]
+[[Category: Almo SC]]
-==Reference==
+[[Category: Fedorov AA]]
-<ref group="xtra">PMID:20369850</ref><references group="xtra"/>
+[[Category: Fedorov EV]]
-[[Category: Methanothermobacter thermautotrophicus]]
+[[Category: Gerlt JA]]
-[[Category: Orotidine-5'-phosphate decarboxylase]]
+[[Category: Wood BM]]
-[[Category: Almo, S C.]]
-[[Category: Fedorov, A A.]]
-[[Category: Fedorov, E V.]]
-[[Category: Gerlt, J A.]]
-[[Category: Wood, B M.]]
-[[Category: 6-azauridine 5'-monophosphate]]
-[[Category: Decarboxylase]]
-[[Category: Lyase]]
-[[Category: Orotidine 5'-monophosphate decarboxylase]]
-[[Category: Pyrimidine biosynthesis]]
-[[Category: S127p]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 16 08:40:25 2010''