1eix

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:03, 7 February 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1eix.jpg|left|200px]]
 
-
{{Structure
+
==STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM E. COLI, CO-CRYSTALLISED WITH THE INHIBITOR BMP==
-
|PDB= 1eix |SIZE=350|CAPTION= <scene name='initialview01'>1eix</scene>, resolution 2.5&Aring;
+
<StructureSection load='1eix' size='340' side='right'caption='[[1eix]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=BMQ:1-(5&#39;-PHOSPHO-BETA-D-RIBOFURANOSYL)BARBITURIC ACID'>BMQ</scene>
+
<table><tr><td colspan='2'>[[1eix]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EIX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EIX FirstGlance]. <br>
-
|ACTIVITY= [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]
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMQ:1-(5-PHOSPHO-BETA-D-RIBOFURANOSYL)BARBITURIC+ACID'>BMQ</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=1eix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eix OCA], [https://pdbe.org/1eix PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eix RCSB], [https://www.ebi.ac.uk/pdbsum/1eix PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eix ProSAT]</span></td></tr>
-
 
+
</table>
-
'''STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM E. COLI, CO-CRYSTALLISED WITH THE INHIBITOR BMP'''
+
== Function ==
-
 
+
[https://www.uniprot.org/uniprot/PYRF_ECOLI PYRF_ECOLI] Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_B]
-
 
+
== Evolutionary Conservation ==
-
==Overview==
+
[[Image:Consurf_key_small.gif|200px|right]]
-
Orotidine 5'-monophosphate decarboxylase (ODCase) catalyzes the decarboxylation of orotidine 5'-monophosphate, the last step in the de novo synthesis of uridine 5'-monophosphate. ODCase is a very proficient enzyme [Radzicka, A., and Wolfenden, R. (1995) Science 267, 90-93], enhancing the reaction rate by a factor of 10(17). This proficiency has been enigmatic, since it is achieved without metal ions or cofactors. Here we present a 2.5 A resolution structure of ODCase complexed with the inhibitor 1-(5'-phospho-beta-D-ribofuranosyl)barbituric acid. It shows a closely packed dimer composed of two alpha/beta-barrels with two shared active sites. The orientation of the orotate moiety of the substrate is unambiguously deduced from the structure, and previously proposed catalytic mechanisms involving protonation of O2 or O4 can be ruled out. The proximity of the OMP carboxylate group with Asp71 appears to be instrumental for the decarboxylation of OMP, either through charge repulsion or through the formation of a very short O.H.O hydrogen bond between the two carboxylate groups.
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==About this Structure==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ei/1eix_consurf.spt"</scriptWhenChecked>
-
1EIX is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EIX OCA].
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==Reference==
+
</jmolCheckbox>
-
Structural basis for the catalytic mechanism of a proficient enzyme: orotidine 5'-monophosphate decarboxylase., Harris P, Navarro Poulsen JC, Jensen KF, Larsen S, Biochemistry. 2000 Apr 18;39(15):4217-24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10757968 10757968]
+
</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=1eix ConSurf].
 +
<div style="clear:both"></div>
 +
__TOC__
 +
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Orotidine-5'-phosphate decarboxylase]]
+
[[Category: Large Structures]]
-
[[Category: Single protein]]
+
[[Category: Harris P]]
-
[[Category: Harris, P.]]
+
[[Category: Jensen KF]]
-
[[Category: Jensen, K F.]]
+
[[Category: Larsen S]]
-
[[Category: Larsen, S.]]
+
[[Category: Poulsen JCN]]
-
[[Category: Poulsen, J C.N.]]
+
-
[[Category: BMQ]]
+
-
[[Category: alpha-beta-barrel]]
+
-
[[Category: homodimer]]
+
-
[[Category: protein-inhibitor complex]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 11:39:43 2008''
+

Current revision

STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM E. COLI, CO-CRYSTALLISED WITH THE INHIBITOR BMP

PDB ID 1eix

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/1eix"
Personal tools