1ec8

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1ec8" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ec8, resolution 1.9&Aring;" /> '''E. COLI GLUCARATE DEH...)
Current revision (07:00, 7 February 2024) (edit) (undo)
 
(16 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1ec8.jpg|left|200px]]<br /><applet load="1ec8" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1ec8, resolution 1.9&Aring;" />
 
-
'''E. COLI GLUCARATE DEHYDRATASE BOUND TO PRODUCT 2,3-DIHYDROXY-5-OXO-HEXANEDIOATE'''<br />
 
-
==Overview==
+
==E. COLI GLUCARATE DEHYDRATASE BOUND TO PRODUCT 2,3-DIHYDROXY-5-OXO-HEXANEDIOATE==
-
D-Glucarate dehydratase (GlucD) from Escherichia coli catalyzes the, dehydration of both D-glucarate and L-idarate as well as their, interconversion via epimerization. GlucD is a member of the mandelate, racemase (MR) subgroup of the enolase superfamily, the members of which, catalyze reactions that are initiated by abstraction of the alpha-proton, of a carboxylate anion substrate. Alignment of the sequence of GlucD with, that of MR reveals a conserved Lys-X-Lys motif and a His-Asp dyad, homologous to the S- and R-specific bases in the active site of MR., Crystals of GlucD have been obtained into which the substrate D-glucarate, and two competitive inhibitors, 4-deoxy-D-glucarate and xylarohydroxamate, could be diffused; D-glucarate is converted to the dehydration product, 5-keto-4-deoxy-D-glucarate (KDG). The structures of these complexes have, been determined and reveal the identities of the ligands for the required, Mg(2+) (Asp(235), Glu(266), and Asn(289)) as well as confirm the expected, presence of Lys(207) and His(339), the catalytic bases that are properly, positioned to abstract the proton from C5 of L-idarate and D-glucarate, respectively. Surprisingly, the C6 carboxylate group of KDG is a bidentate, ligand to the Mg(2+), with the resulting geometry of the bound KDG, suggesting that stereochemical roles of Lys(207) and His(339) are reversed, from the predictions made on the basis of the established, structure-function relationships for the MR-catalyzed reaction. The, catalytic roles of these residues have been examined by characterization, of mutant enzymes, although we were unable to use these to demonstrate the, catalytic independence of Lys(207) and His(339) as was possible for the, homologous Lys(166) and His(297) in the MR-catalyzed reaction.
+
<StructureSection load='1ec8' size='340' side='right'caption='[[1ec8]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[1ec8]] 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=1EC8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EC8 FirstGlance]. <br>
-
1EC8 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with MG, GLR and IPA as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Glucarate_dehydratase Glucarate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.40 4.2.1.40] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EC8 OCA].
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
-
 
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLR:2,3-DIHYDROXY-5-OXO-HEXANEDIOATE'>GLR</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-
==Reference==
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ec8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ec8 OCA], [https://pdbe.org/1ec8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ec8 RCSB], [https://www.ebi.ac.uk/pdbsum/1ec8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ec8 ProSAT]</span></td></tr>
-
Evolution of enzymatic activities in the enolase superfamily: crystallographic and mutagenesis studies of the reaction catalyzed by D-glucarate dehydratase from Escherichia coli., Gulick AM, Hubbard BK, Gerlt JA, Rayment I, Biochemistry. 2000 Apr 25;39(16):4590-602. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10769114 10769114]
+
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/GUDD_ECOLI GUDD_ECOLI] Catalyzes the dehydration of glucarate to 5-keto-4-deoxy-D-glucarate (5-kdGluc). Also acts on L-idarate.
 +
== 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/ec/1ec8_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=1ec8 ConSurf].
 +
<div style="clear:both"></div>
 +
__TOC__
 +
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Glucarate dehydratase]]
+
[[Category: Large Structures]]
-
[[Category: Single protein]]
+
[[Category: Gerlt JA]]
-
[[Category: Gerlt, J.A.]]
+
[[Category: Gulick AM]]
-
[[Category: Gulick, A.M.]]
+
[[Category: Hubbard BK]]
-
[[Category: Hubbard, B.K.]]
+
[[Category: Rayment I]]
-
[[Category: Rayment, I.]]
+
-
[[Category: GLR]]
+
-
[[Category: IPA]]
+
-
[[Category: MG]]
+
-
[[Category: glucarate dehydratase enolase enzyme superfamily tim barrel (beta/alpha)7beta barrel]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:53:14 2007''
+

Current revision

E. COLI GLUCARATE DEHYDRATASE BOUND TO PRODUCT 2,3-DIHYDROXY-5-OXO-HEXANEDIOATE

PDB ID 1ec8

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/1ec8"
Personal tools