1kly

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1kly" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kly, resolution 1.50&Aring;" /> '''Orotidine monophosph...)
Current revision (07:25, 14 February 2024) (edit) (undo)
 
(16 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1kly.gif|left|200px]]<br /><applet load="1kly" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1kly, resolution 1.50&Aring;" />
 
-
'''Orotidine monophosphate decarboxylase D70G mutant complexed with 6-azaUMP'''<br />
 
-
==Overview==
+
==Orotidine monophosphate decarboxylase D70G mutant complexed with 6-azaUMP==
-
The crystal structures of orotidine 5'-monophosphate decarboxylases from, four different sources have been published recently. However, the detailed, mechanism of catalysis of the most proficient enzyme known to date remains, elusive. As the ligand-protein interactions at the orotate binding site, are crucial to the understanding of this enzyme, we mutated several of the, residues surrounding the aromatic part of the substrate, individually and, in combination. The ensuing effects on enzyme structure and stability were, characterized by X-ray crystallography of inhibitor, product, or substrate, complexes and by chemical denaturation with guanidine hydrochloride, respectively. The results are consistent with the residues K42D70K72D75B, being charged and forming an 'alternate charge network' around the, reactive part of the substrate. In addition to exerting charge-charge, repulsion on the orotate carboxylate, Asp70 also makes a crucial, contribution to enzyme stability. Consequently, orotidine 5'-monophosphate, decarboxylases seem to require the presence of a negative charge at this, position for catalysis as well as for correct and stable folding.
+
<StructureSection load='1kly' size='340' side='right'caption='[[1kly]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1kly]] 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=1KLY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KLY 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]] 1.5&#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>
 +
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kly OCA], [https://pdbe.org/1kly PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kly RCSB], [https://www.ebi.ac.uk/pdbsum/1kly PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kly 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/kl/1kly_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=1kly ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1KLY 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 UP6 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=1KLY OCA].
+
*[[Uridine 5'-monophosphate synthase 3D structures|Uridine 5'-monophosphate synthase 3D structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
Mapping the active site-ligand interactions of orotidine 5'-monophosphate decarboxylase by crystallography., Wu N, Gillon W, Pai EF, Biochemistry. 2002 Mar 26;41(12):4002-11. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11900543 11900543]
+
[[Category: Large Structures]]
[[Category: Methanothermobacter thermautotrophicus]]
[[Category: Methanothermobacter thermautotrophicus]]
-
[[Category: Orotidine-5'-phosphate decarboxylase]]
+
[[Category: Gillon W]]
-
[[Category: Single protein]]
+
[[Category: Pai EF]]
-
[[Category: Gillon, W.]]
+
[[Category: Wu N]]
-
[[Category: Pai, E.F.]]
+
-
[[Category: Wu, N.]]
+
-
[[Category: UP6]]
+
-
[[Category: tim barrel]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:21:01 2007''
+

Current revision

Orotidine monophosphate decarboxylase D70G mutant complexed with 6-azaUMP

PDB ID 1kly

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1kly"
Personal tools