1u80: Difference between revisions

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New page: left|200px<br /><applet load="1u80" size="450" color="white" frame="true" align="right" spinBox="true" caption="1u80, resolution 2.85Å" /> '''Phosphopantothenoylc...
 
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[[Image:1u80.gif|left|200px]]<br /><applet load="1u80" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1u80, resolution 2.85&Aring;" />
'''Phosphopantothenoylcysteine synthetase from E. coli, CMP complex'''<br />


==Overview==
==Phosphopantothenoylcysteine synthetase from E. coli, CMP complex==
Phosphopantothenoylcysteine (PPC) synthetase forms a peptide bond between, 4'-phosphopantothenate and cysteine in coenzyme A biosynthesis. PPC, synthetases fall into two classes: eukaryotic, ATP-dependent and, eubacterial, CTP-dependent enzymes. We describe the first crystal, structure of E. coli PPC synthetase as a prototype of bacterial, CTP-dependent PPC synthetases. Structures of the apo-form and the, synthetase complexed with CTP, the activated acyl-intermediate, 4'-phosphopantothenoyl-CMP, and with the reaction product CMP provide, snapshots along the reaction pathway and detailed insight into substrate, binding and the reaction mechanism of peptide bond formation. Binding of, the phosphopantothenate moiety of the acyl-intermediate in a cleft at the, C-terminal end of the central beta sheet of the dinucleotide binding fold, is accomplished by an otherwise flexible flap. A second disordered loop, may control access of cysteine to the active site. The conservation of, functionalities involved in substrate binding and catalysis provides, insight into similarities and differences of prokaryotic and eukaryotic, PPC synthetases.
<StructureSection load='1u80' size='340' side='right'caption='[[1u80]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1u80]] is a 3 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=1U80 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U80 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.85&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=1u80 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u80 OCA], [https://pdbe.org/1u80 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u80 RCSB], [https://www.ebi.ac.uk/pdbsum/1u80 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u80 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/COABC_ECOLI COABC_ECOLI] Catalyzes two steps in the biosynthesis of coenzyme A. In the first step cysteine is conjugated to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, in the latter compound is decarboxylated to form 4'-phosphopantotheine.
== 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/u8/1u80_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=1u80 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Phosphopantothenoylcysteine (PPC) synthetase forms a peptide bond between 4'-phosphopantothenate and cysteine in coenzyme A biosynthesis. PPC synthetases fall into two classes: eukaryotic, ATP-dependent and eubacterial, CTP-dependent enzymes. We describe the first crystal structure of E. coli PPC synthetase as a prototype of bacterial, CTP-dependent PPC synthetases. Structures of the apo-form and the synthetase complexed with CTP, the activated acyl-intermediate, 4'-phosphopantothenoyl-CMP, and with the reaction product CMP provide snapshots along the reaction pathway and detailed insight into substrate binding and the reaction mechanism of peptide bond formation. Binding of the phosphopantothenate moiety of the acyl-intermediate in a cleft at the C-terminal end of the central beta sheet of the dinucleotide binding fold is accomplished by an otherwise flexible flap. A second disordered loop may control access of cysteine to the active site. The conservation of functionalities involved in substrate binding and catalysis provides insight into similarities and differences of prokaryotic and eukaryotic PPC synthetases.


==About this Structure==
Structural basis of CTP-dependent peptide bond formation in coenzyme A biosynthesis catalyzed by Escherichia coli PPC synthetase.,Stanitzek S, Augustin MA, Huber R, Kupke T, Steinbacher S Structure. 2004 Nov;12(11):1977-88. PMID:15530362<ref>PMID:15530362</ref>
1U80 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 PO4 and C5P as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Phosphopantothenate--cysteine_ligase Phosphopantothenate--cysteine ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.5 6.3.2.5] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1U80 OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Structural basis of CTP-dependent peptide bond formation in coenzyme A biosynthesis catalyzed by Escherichia coli PPC synthetase., Stanitzek S, Augustin MA, Huber R, Kupke T, Steinbacher S, Structure. 2004 Nov;12(11):1977-88. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15530362 15530362]
</div>
<div class="pdbe-citations 1u80" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Phosphopantothenate--cysteine ligase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Augustin MA]]
[[Category: Augustin, M.A.]]
[[Category: Huber R]]
[[Category: Huber, R.]]
[[Category: Kupke T]]
[[Category: Kupke, T.]]
[[Category: Stanitzek S]]
[[Category: Stanitzek, S.]]
[[Category: Steinbacher S]]
[[Category: Steinbacher, S.]]
[[Category: C5P]]
[[Category: PO4]]
[[Category: coenzyme a biosynthesis]]
 
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Latest revision as of 07:30, 25 October 2023

Phosphopantothenoylcysteine synthetase from E. coli, CMP complex

1u80, resolution 2.85Å

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