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3pnl

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Current revision (13:32, 1 March 2024) (edit) (undo)
 
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<StructureSection load='3pnl' size='340' side='right'caption='[[3pnl]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='3pnl' size='340' side='right'caption='[[3pnl]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3pnl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PNL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PNL FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3pnl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PNL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PNL FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3pnq|3pnq]], [[3pnk|3pnk]], [[3pnm|3pnm]], [[3pno|3pno]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b1200, dhaK, JW5187, ycgT ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), b1199, dhaL, JW5186, ycgS ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3pnl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pnl OCA], [https://pdbe.org/3pnl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pnl RCSB], [https://www.ebi.ac.uk/pdbsum/3pnl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pnl ProSAT]</span></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=3pnl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pnl OCA], [https://pdbe.org/3pnl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pnl RCSB], [https://www.ebi.ac.uk/pdbsum/3pnl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pnl ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/DHAK_ECOLI DHAK_ECOLI]] Dihydroxyacetone binding subunit of the dihydroxyacetone kinase, which is responsible for phosphorylating dihydroxyacetone. Binds covalently dihydroxyacetone in hemiaminal linkage. Acts also as a corepressor of DhaR by binding to its sensor domain, in the absence of dihydroxyacetone. [[https://www.uniprot.org/uniprot/DHAL_ECOLI DHAL_ECOLI]] ADP-binding subunit of the dihydroxyacetone kinase, which is responsible for phosphorylating dihydroxyacetone. DhaL-ADP receives a phosphoryl group from DhaM and transmits it to dihydroxyacetone. DhaL-ADP acts also as a coactivator by binding to the sensor domain of DhaR. DhaL-ATP is inactive.
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[https://www.uniprot.org/uniprot/DHAK_ECOLI DHAK_ECOLI] Dihydroxyacetone binding subunit of the dihydroxyacetone kinase, which is responsible for phosphorylating dihydroxyacetone. Binds covalently dihydroxyacetone in hemiaminal linkage. Acts also as a corepressor of DhaR by binding to its sensor domain, in the absence of dihydroxyacetone.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The Escherichia coli dihydroxyacetone (Dha) kinase is an unusual kinase because (i) it uses the phosphoenolpyruvate carbohydrate: phosphotransferase system (PTS) as the source of high-energy phosphate, (ii) the active site is formed by two subunits, and (iii) the substrate is covalently bound to His218(K)* of the DhaK subunit. The PTS transfers phosphate to DhaM, which in turn phosphorylates the permanently bound ADP coenzyme of DhaL. This phosphoryl group is subsequently transferred to the Dha substrate bound to DhaK. Here we report the crystal structure of the E. coli Dha kinase complex, DhaK-DhaL. The structure of the complex reveals that DhaK undergoes significant conformational changes to accommodate binding of DhaL. Combined mutagenesis and enzymatic activity studies of kinase mutants allow us to propose a catalytic mechanism for covalent Dha binding, phosphorylation, and release of the Dha-phosphate product. Our results show that His56(K) is involved in formation of the covalent hemiaminal bond with Dha. The structure of H56N(K) with noncovalently bound substrate reveals a somewhat different positioning of Dha in the binding pocket as compared to covalently bound Dha, showing that the covalent attachment to His218(K) orients the substrate optimally for phosphoryl transfer. Asp109(K) is critical for activity, likely acting as a general base activating the gamma-OH of Dha. Our results provide a comprehensive picture of the roles of the highly conserved active site residues of dihydroxyacetone kinases.
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Structural and mechanistic insight into covalent substrate binding by Escherichia coli dihydroxyacetone kinase.,Shi R, McDonald L, Cui Q, Matte A, Cygler M, Ekiel I Proc Natl Acad Sci U S A. 2011 Jan 5. PMID:21209328<ref>PMID:21209328</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3pnl" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Ecoli]]
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[[Category: Escherichia coli K-12]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Structural genomic]]
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[[Category: Cygler M]]
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[[Category: Cygler, M]]
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[[Category: Ekiel I]]
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[[Category: Ekiel, I]]
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[[Category: Matte A]]
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[[Category: Matte, A]]
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[[Category: McDonald L]]
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[[Category: McDonald, L]]
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[[Category: Shi R]]
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[[Category: Shi, R]]
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[[Category: Bsgi]]
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[[Category: Dha kinase]]
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[[Category: Transferase]]
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Current revision

Crystal Structure of E.coli Dha kinase DhaK-DhaL complex

PDB ID 3pnl

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