1ecq: Difference between revisions

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[[Image:1ecq.jpg|left|200px]]


{{Structure
==E. COLI GLUCARATE DEHYDRATASE BOUND TO 4-DEOXYGLUCARATE==
|PDB= 1ecq |SIZE=350|CAPTION= <scene name='initialview01'>1ecq</scene>, resolution 2.0&Aring;
<StructureSection load='1ecq' size='340' side='right'caption='[[1ecq]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=DXG:4-DEOXYGLUCARATE'>DXG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> and <scene name='pdbligand=IPA:ISOPROPYL ALCOHOL'>IPA</scene>
<table><tr><td colspan='2'>[[1ecq]] 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=1ECQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ECQ FirstGlance]. <br>
|ACTIVITY= [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]  
</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&#8491;</td></tr>
|GENE=
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DXG:4-DEOXYGLUCARATE'>DXG</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1ecq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ecq OCA], [https://pdbe.org/1ecq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ecq RCSB], [https://www.ebi.ac.uk/pdbsum/1ecq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ecq ProSAT]</span></td></tr>
 
</table>
'''E. COLI GLUCARATE DEHYDRATASE BOUND TO 4-DEOXYGLUCARATE'''
== 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 ==
==Overview==
[[Image:Consurf_key_small.gif|200px|right]]
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.
Check<jmol>
 
  <jmolCheckbox>
==About this Structure==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ec/1ecq_consurf.spt"</scriptWhenChecked>
1ECQ 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=1ECQ OCA].  
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==Reference==
  </jmolCheckbox>
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://www.ncbi.nlm.nih.gov/pubmed/10769114 10769114]
</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=1ecq 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: DXG]]
[[Category: IPA]]
[[Category: MG]]
[[Category: glucarate dehydratase enolase enzyme superfamily tim barrel (beta/alpha)7beta barrel]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:53:46 2008''

Latest revision as of 10:01, 7 February 2024

E. COLI GLUCARATE DEHYDRATASE BOUND TO 4-DEOXYGLUCARATEE. COLI GLUCARATE DEHYDRATASE BOUND TO 4-DEOXYGLUCARATE

Structural highlights

1ecq is a 4 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GUDD_ECOLI Catalyzes the dehydration of glucarate to 5-keto-4-deoxy-D-glucarate (5-kdGluc). Also acts on L-idarate.

Evolutionary Conservation

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

1ecq, resolution 2.00Å

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