2zz4

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{{Seed}}
 
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[[Image:2zz4.png|left|200px]]
 
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==Covalent complex of orotidine monophosphate decarboxylase D75N mutant from M. thermoautotrophicum with 6-cyano-UMP==
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The line below this paragraph, containing "STRUCTURE_2zz4", creates the "Structure Box" on the page.
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<StructureSection load='2zz4' size='340' side='right'caption='[[2zz4]], [[Resolution|resolution]] 1.67&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2zz4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZZ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZZ4 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.67&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6CN:6-CYANOURIDINE+5-PHOSPHATE'>6CN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
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{{STRUCTURE_2zz4| PDB=2zz4 | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zz4 OCA], [https://pdbe.org/2zz4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zz4 RCSB], [https://www.ebi.ac.uk/pdbsum/2zz4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zz4 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zz/2zz4_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=2zz4 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Crystal structures of substrate-product complexes of Methanobacterium thermoautotrophicum orotidine 5'-monophosphate decarboxylase, obtained at various steps in its catalysis of the unusual transformation of 6-cyano-uridine 5'-monophosphate (UMP) into barbituric acid ribosyl monophosphate, show that the cyano substituent of the substrate, when bound to the active site, is first bent significantly from the plane of the pyrimidine ring and then replaced by an oxygen atom. Although the K72A and D70A/K72A mutants are either catalytically impaired or even completely inactive, they still display bending of the C6 substituent. Interestingly, high-resolution structures of the D70A and D75N mutants revealed a covalent bond between C6 of UMP and the Lys72 side chain after the -CN moiety's release. The same covalent bond was observed when the native enzyme was incubated with 6-azido-UMP and 6-iodo-UMP; in contrast, the K72A mutant transformed 6-iodo-UMP to barbituric acid ribosyl 5'-monophosphate. These results demonstrate that, given a suitable environment, native orotidine 5'-monophosphate decarboxylase and several of its mutants are not restricted to the physiologically relevant decarboxylation; they are able to catalyze even nucleophilic substitution reactions but consistently maintain distortion on the C6 substituent as an important feature of catalysis.
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===Covalent complex of orotidine monophosphate decarboxylase D75N mutant from M. thermoautotrophicum with 6-cyano-UMP===
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Structural characterization of the molecular events during a slow substrate-product transition in orotidine 5'-monophosphate decarboxylase.,Fujihashi M, Wei L, Kotra LP, Pai EF J Mol Biol. 2009 Apr 17;387(5):1199-210. Epub 2009 Feb 21. PMID:19236876<ref>PMID:19236876</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2zz4" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_19236876}}, adds the Publication Abstract to the page
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*[[Uridine 5'-monophosphate synthase 3D structures|Uridine 5'-monophosphate synthase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 19236876 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19236876}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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2ZZ4 is a 2 chains structure of 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=2ZZ4 OCA].
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==Reference==
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<ref group="xtra">PMID:19236876</ref><references group="xtra"/>
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[[Category: Methanothermobacter thermautotrophicus]]
[[Category: Methanothermobacter thermautotrophicus]]
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[[Category: Orotidine-5'-phosphate decarboxylase]]
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[[Category: Fujihashi M]]
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[[Category: Fujihashi, M.]]
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[[Category: Pai EF]]
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[[Category: Pai, E F.]]
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[[Category: Decarboxylase]]
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[[Category: Lyase]]
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[[Category: Odcase]]
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[[Category: Ompdc]]
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[[Category: Ompdcase]]
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[[Category: Pyrimidine biosynthesis]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 16 08:24:18 2009''
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Current revision

Covalent complex of orotidine monophosphate decarboxylase D75N mutant from M. thermoautotrophicum with 6-cyano-UMP

PDB ID 2zz4

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