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New page: left|200px<br /><applet load="1eaa" size="450" color="white" frame="true" align="right" spinBox="true" caption="1eaa, resolution 2.6Å" /> '''ATOMIC STRUCTURE OF T...
 
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[[Image:1eaa.jpg|left|200px]]<br /><applet load="1eaa" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1eaa, resolution 2.6&Aring;" />
'''ATOMIC STRUCTURE OF THE CUBIC CORE OF THE PYRUVATE DEHYDROGENASE MULTIENZYME COMPLEX'''<br />


==Overview==
==ATOMIC STRUCTURE OF THE CUBIC CORE OF THE PYRUVATE DEHYDROGENASE MULTIENZYME COMPLEX==
The catalytic domain of dihydrolipoyl transacetylase (E2pCD) forms the, core of the pyruvate dehydrogenase multienzyme complex and catalyzes the, acetyltransferase reaction using acetylCoA as acetyl donor and, dihydrolipoamide (Lip(SH)2) as acceptor. The crystal structures of six, complexes and derivatives of Azotobacter vinelandii E2pCD were solved. The, binary complexes of the enzyme with CoA and Lip(SH)2 were determined at, 2.6- and 3.0-A resolutions, respectively. The two substrates are found in, an extended conformation at the two opposite entrances of the 30 A long, channel which runs at the interface between two 3-fold-related subunits, and forms the catalytic center. The reactive thiol groups of both, substrates are within hydrogen-bond distance from the side chain of His, 610. This fact supports the indication, derived from the similarity with, chloramphenicol acetyl transferase, that the histidine side chain acts as, general-base catalyst in the deprotonation of the reactive thiol of CoA., The conformation of Asn 614 appears to be dependent on the protonation, state of the active site histidine, whose function as base catalyst is, modulated in this way. Studies on E2pCD soaked in a high concentration of, dithionite lead to the structure of the binary complex between E2pCD and, hydrogen sulfite solved at 2.3-A resolution. It appears that the anion is, bound in the middle of the catalytic center and is therefore capable of, hosting and stabilizing a negative charge, which is of special interest, since the reaction catalyzed by E2pCD is thought to proceed via a, negatively charged tetrahedral intermediate. The structure of the binary, complex between E2pCD and hydrogen sulfite suggests that transition-state, stabilization can be provided by a direct hydrogen bond between the side, chain of Ser 558 and the oxy anion of the putative intermediate. In the, binary complex with CoA, the hydroxyl group of Ser 558 is hydrogen bonded, to the nitrogen atom of one of the two peptide-like units of the, substrate. Thus, CoA itself is involved in keeping the Ser hydroxyl group, in the proper position for transition-state stabilization. Quite, unexpectedly, the structure at 2.6-A resolution of a ternary complex in, which CoA and Lip(SH)2 are simultaneously bound to E2pCD reveals that CoA, has an alternative, nonproductive binding mode. In this abortive ternary, complex, CoA adopts a helical conformation with two intramolecular, hydrogen bonds and the reactive sulfur of the pantetheine arm positioned, 12 A away from the active site residues involved in the transferase, reaction.(ABSTRACT TRUNCATED AT 400 WORDS)
<StructureSection load='1eaa' size='340' side='right'caption='[[1eaa]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1eaa]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. The September 2012 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Pyruvate Dehydrogenase Complex''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2012_9 10.2210/rcsb_pdb/mom_2012_9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EAA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EAA FirstGlance]. <br>
1EAA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Active as [http://en.wikipedia.org/wiki/Dihydrolipoyllysine-residue_acetyltransferase Dihydrolipoyllysine-residue acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.12 2.3.1.12] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EAA 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]] 2.6&#8491;</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=1eaa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eaa OCA], [https://pdbe.org/1eaa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eaa RCSB], [https://www.ebi.ac.uk/pdbsum/1eaa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eaa ProSAT]</span></td></tr>
==Reference==
</table>
Crystallographic analysis of substrate binding and catalysis in dihydrolipoyl transacetylase (E2p)., Mattevi A, Obmolova G, Kalk KH, Teplyakov A, Hol WG, Biochemistry. 1993 Apr 20;32(15):3887-901. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8471601 8471601]
== Function ==
[https://www.uniprot.org/uniprot/ODP2_AZOVI ODP2_AZOVI] The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2). It contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase (E3).
== 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/ea/1eaa_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=1eaa ConSurf].
<div style="clear:both"></div>
__TOC__
</StructureSection>
[[Category: Azotobacter vinelandii]]
[[Category: Azotobacter vinelandii]]
[[Category: Dihydrolipoyllysine-residue acetyltransferase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Pyruvate Dehydrogenase Complex]]
[[Category: Hol, W.G.J.]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Mattevi, A.]]
[[Category: Hol WGJ]]
[[Category: dihydrolipoamide acetyltransferase]]
[[Category: Mattevi A]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:51:07 2007''

Latest revision as of 07:00, 7 February 2024

ATOMIC STRUCTURE OF THE CUBIC CORE OF THE PYRUVATE DEHYDROGENASE MULTIENZYME COMPLEX

1eaa, resolution 2.60Å

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