1km6

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:26, 14 February 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1km6.gif|left|200px]]
 
-
{{Structure
+
==Crystal structure of ODCase mutant D70AK72A complexed with OMP==
-
|PDB= 1km6 |SIZE=350|CAPTION= <scene name='initialview01'>1km6</scene>, resolution 1.50&Aring;
+
<StructureSection load='1km6' size='340' side='right'caption='[[1km6]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=OMP:OROTIDINE-5&#39;-MONOPHOSPHATE'>OMP</scene>
+
<table><tr><td colspan='2'>[[1km6]] 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=1KM6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KM6 FirstGlance]. <br>
-
|ACTIVITY= <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><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>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OMP:OROTIDINE-5-MONOPHOSPHATE'>OMP</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1km6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1km6 OCA], [https://pdbe.org/1km6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1km6 RCSB], [https://www.ebi.ac.uk/pdbsum/1km6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1km6 ProSAT]</span></td></tr>
-
|RELATEDENTRY=[[1kly|1KLY]], [[1klz|1KLZ]], [[1km0|1KM0]], [[1km1|1KM1]], [[1km2|1KM2]], [[1km3|1KM3]], [[1km4|1KM4]], [[1km5|1KM5]]
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1km6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1km6 OCA], [http://www.ebi.ac.uk/pdbsum/1km6 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1km6 RCSB]</span>
+
== 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/km/1km6_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=1km6 ConSurf].
 +
<div style="clear:both"></div>
-
'''Crystal structure of ODCase mutant D70AK72A complexed with OMP'''
+
==See Also==
-
 
+
*[[Uridine 5'-monophosphate synthase 3D structures|Uridine 5'-monophosphate synthase 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
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.
+
[[Category: Large Structures]]
-
 
+
-
==About this Structure==
+
-
1KM6 is a [[Single protein]] structure of sequence 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=1KM6 OCA].
+
-
 
+
-
==Reference==
+
-
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://www.ncbi.nlm.nih.gov/pubmed/11900543 11900543]
+
[[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: tim barrel]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:50:33 2008''
+

Current revision

Crystal structure of ODCase mutant D70AK72A complexed with OMP

PDB ID 1km6

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/1km6"
Personal tools