3w07

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{{STRUCTURE_3w07| PDB=3w07 | SCENE= }}
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==Atomic resolution structure of orotidine 5'-monophosphate decarboxylase from Methanothermobacter thermoautotrophicus bound with UMP.==
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===Atomic resolution structure of orotidine 5'-monophosphate decarboxylase from Methanothermobacter thermoautotrophicus bound with UMP.===
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<StructureSection load='3w07' size='340' side='right' caption='[[3w07]], [[Resolution|resolution]] 1.03&Aring;' scene=''>
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{{ABSTRACT_PUBMED_23395822}}
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3w07]] is a 1 chain structure with sequence from [http://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=3W07 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3W07 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1loq|1loq]], [[3g1d|3g1d]]</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pyrF, MTH_129 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=187420 Methanothermobacter thermautotrophicus str. Delta H])</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3w07 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w07 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3w07 RCSB], [http://www.ebi.ac.uk/pdbsum/3w07 PDBsum]</span></td></tr>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Orotidine 5'-monophosphate decarboxylase (ODCase) accelerates the decarboxylation of its substrate by 17 orders of magnitude. One argument brought forward against steric/electrostatic repulsion causing substrate distortion at the carboxylate substituent as part of the catalysis has been the weak binding affinity of the decarboxylated product (UMP). The crystal structure of the UMP complex of ODCase at atomic resolution (1.03 A) shows steric competition between the product UMP and the side chain of a catalytic lysine residue. Surface plasmon resonance analysis indicates that UMP binds 5 orders of magnitude more tightly to a mutant in which the interfering side chain has been removed than to wild-type ODCase. These results explain the low affinity of UMP and counter a seemingly very strong argument against a contribution of substrate distortion to the catalytic reaction mechanism of ODCase.
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==Function==
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Atomic resolution structure of the orotidine 5'-monophosphate decarboxylase product complex combined with surface plasmon resonance analysis: implications for the catalytic mechanism.,Fujihashi M, Mito K, Pai EF, Miki K J Biol Chem. 2013 Mar 29;288(13):9011-6. doi: 10.1074/jbc.M112.427252. Epub 2013 , Feb 10. PMID:23395822<ref>PMID:23395822</ref>
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[[http://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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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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[[3w07]] is a 1 chain structure with sequence from [http://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=3W07 OCA].
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</div>
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== References ==
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==Reference==
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<references/>
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<ref group="xtra">PMID:023395822</ref><references group="xtra"/><references/>
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__TOC__
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</StructureSection>
[[Category: Methanothermobacter thermautotrophicus str. delta h]]
[[Category: Methanothermobacter thermautotrophicus str. delta h]]
[[Category: Orotidine-5'-phosphate decarboxylase]]
[[Category: Orotidine-5'-phosphate decarboxylase]]
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[[Category: Fujihashi, M.]]
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[[Category: Fujihashi, M]]
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[[Category: Miki, K.]]
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[[Category: Miki, K]]
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[[Category: Pai, E F.]]
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[[Category: Pai, E F]]
[[Category: Lyase]]
[[Category: Lyase]]
[[Category: Orotidine 5'-monophosphate decarboxylase]]
[[Category: Orotidine 5'-monophosphate decarboxylase]]

Revision as of 07:28, 21 December 2014

Atomic resolution structure of orotidine 5'-monophosphate decarboxylase from Methanothermobacter thermoautotrophicus bound with UMP.

3w07, resolution 1.03Å

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