1n3b: Difference between revisions

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<StructureSection load='1n3b' size='340' side='right'caption='[[1n3b]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='1n3b' size='340' side='right'caption='[[1n3b]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1n3b]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N3B OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1N3B FirstGlance]. <br>
<table><tr><td colspan='2'>[[1n3b]] 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=1N3B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N3B FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">COAE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1n3b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n3b OCA], [https://pdbe.org/1n3b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n3b RCSB], [https://www.ebi.ac.uk/pdbsum/1n3b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n3b ProSAT], [https://www.topsan.org/Proteins/BSGI/1n3b TOPSAN]</span></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dephospho-CoA_kinase Dephospho-CoA kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.24 2.7.1.24] </span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1n3b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n3b OCA], [http://pdbe.org/1n3b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n3b RCSB], [http://www.ebi.ac.uk/pdbsum/1n3b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1n3b ProSAT], [http://www.topsan.org/Proteins/BSGI/1n3b TOPSAN]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/COAE_ECOLI COAE_ECOLI]] Catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A.  
[https://www.uniprot.org/uniprot/COAE_ECOLI COAE_ECOLI] Catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1n3b ConSurf].
</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=1n3b ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Coenzyme A (CoA) is an essential cofactor used in a wide variety of biochemical pathways. The final step in the biosynthesis of CoA is catalyzed by dephosphocoenzyme A kinase (DPCK, E.C. 2.7.1.24). Here we report the crystal structure of DPCK from Escherichia coli at 1.8 A resolution. This enzyme forms a tightly packed trimer in its crystal state, in contrast to its observed monomeric structure in solution and to the monomeric, homologous DPCK structure from Haemophilus influenzae. We have confirmed the existence of the trimeric form of the enzyme in solution using gel filtration chromatography measurements. Dephospho-CoA kinase is structurally similar to many nucleoside kinases and other P-loop-containing nucleotide triphosphate hydrolases, despite having negligible sequence similarity to these enzymes. Each monomer consists of five parallel beta-strands flanked by alpha-helices, with an ATP-binding site formed by a P-loop motif. Orthologs of the E. coli DPCK sequence exist in a wide range of organisms, including humans. Multiple alignment of orthologous DPCK sequences reveals a set of highly conserved residues in the vicinity of the nucleotide/CoA binding site.
Crystal structure of a trimeric form of dephosphocoenzyme A kinase from Escherichia coli.,O'Toole N, Barbosa JA, Li Y, Hung LW, Matte A, Cygler M Protein Sci. 2003 Feb;12(2):327-36. PMID:12538896<ref>PMID:12538896</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1n3b" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus coli migula 1895]]
[[Category: Escherichia coli]]
[[Category: Dephospho-CoA kinase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Structural genomic]]
[[Category: Barbosa JARG]]
[[Category: Barbosa, J A.R G]]
[[Category: Cygler M]]
[[Category: Cygler, M]]
[[Category: Hung L-W]]
[[Category: Hung, L W]]
[[Category: Li Y]]
[[Category: Li, Y]]
[[Category: Matte A]]
[[Category: Matte, A]]
[[Category: O'Toole N]]
[[Category: Toole, N O]]
[[Category: Alpha/beta]]
[[Category: Bsgi]]
[[Category: P-loop]]
[[Category: Transferase]]
[[Category: Trimer]]

Revision as of 08:45, 10 April 2024

Crystal Structure of Dephosphocoenzyme A kinase from Escherichia coli

1n3b, resolution 1.80Å

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