1lor: Difference between revisions

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New page: left|200px<br /><applet load="1lor" size="450" color="white" frame="true" align="right" spinBox="true" caption="1lor, resolution 1.60Å" /> '''crystal structure of...
 
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[[Image:1lor.jpg|left|200px]]<br /><applet load="1lor" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1lor, resolution 1.60&Aring;" />
'''crystal structure of orotidine 5'-monophosphate complexed with BMP'''<br />


==Overview==
==crystal structure of orotidine 5'-monophosphate complexed with BMP==
The crystal structures of the enzyme orotidine-5'-monophosphate, decarboxylase from Methanobacterium thermoautotrophicum complexed with its, product UMP and the inhibitors 6-hydroxyuridine 5'-phosphate (BMP), XMP, and CMP are reported. A mutant version of the protein, in which four, residues of the flexible phosphate-binding loop (180)Gly-Gly(190) were, removed and Arg(203) was replaced by alanine, was also analyzed. The XMP, and CMP complexes reveal a ligand-binding mode that is distinct from the, one identified previously with the aromatic rings located outside the, binding pocket. A potential pathway for ligand binding is discussed.
<StructureSection load='1lor' size='340' side='right'caption='[[1lor]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1lor]] is a 1 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=1LOR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LOR 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]] 1.6&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMP:6-HYDROXYURIDINE-5-PHOSPHATE'>BMP</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=1lor FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lor OCA], [https://pdbe.org/1lor PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lor RCSB], [https://www.ebi.ac.uk/pdbsum/1lor PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lor 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/lo/1lor_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=1lor ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1LOR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus] with BMP as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1LOR OCA].
*[[Uridine 5'-monophosphate synthase 3D structures|Uridine 5'-monophosphate synthase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Crystal structures of inhibitor complexes reveal an alternate binding mode in orotidine-5'-monophosphate decarboxylase., Wu N, Pai EF, J Biol Chem. 2002 Aug 2;277(31):28080-7. Epub 2002 May 13. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12011084 12011084]
[[Category: Large Structures]]
[[Category: Methanothermobacter thermautotrophicus]]
[[Category: Methanothermobacter thermautotrophicus]]
[[Category: Orotidine-5'-phosphate decarboxylase]]
[[Category: Pai EF]]
[[Category: Single protein]]
[[Category: Wu N]]
[[Category: Pai, E.F.]]
[[Category: Wu, N.]]
[[Category: BMP]]
[[Category: tim barrel]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 20:44:06 2007''

Latest revision as of 10:34, 14 February 2024

crystal structure of orotidine 5'-monophosphate complexed with BMPcrystal structure of orotidine 5'-monophosphate complexed with BMP

Structural highlights

1lor is a 1 chain structure with sequence from Methanothermobacter thermautotrophicus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.6Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PYRF_METTH Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_A]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1lor, resolution 1.60Å

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