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| | ==Linkage between the Bacterial Acid Stress and Stringent Responses: The Structure of the Inducible Lysine Decarboxylase== | | ==Linkage between the Bacterial Acid Stress and Stringent Responses: The Structure of the Inducible Lysine Decarboxylase== |
| - | <StructureSection load='3q16' size='340' side='right' caption='[[3q16]], [[Resolution|resolution]] 4.10Å' scene=''> | + | <StructureSection load='3q16' size='340' side='right'caption='[[3q16]], [[Resolution|resolution]] 4.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3q16]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q16 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3Q16 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3q16]] is a 5 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=3Q16 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q16 FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</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]] 4.1Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cadA, ldcI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysine_decarboxylase Lysine decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.18 4.1.1.18] </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=3q16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q16 OCA], [https://pdbe.org/3q16 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q16 RCSB], [https://www.ebi.ac.uk/pdbsum/3q16 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q16 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3q16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q16 OCA], [http://pdbe.org/3q16 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3q16 RCSB], [http://www.ebi.ac.uk/pdbsum/3q16 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3q16 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/LDCI_ECOLI LDCI_ECOLI]] Plays a role in pH homeostasis by consuming protons and neutralizing the acidic by-products of carbohydrate fermentation. | + | [https://www.uniprot.org/uniprot/LDCI_ECOLI LDCI_ECOLI] Plays a role in pH homeostasis by consuming protons and neutralizing the acidic by-products of carbohydrate fermentation. |
| - | <div style="background-color:#fffaf0;">
| + | |
| - | == Publication Abstract from PubMed ==
| + | |
| - | The Escherichia coli inducible lysine decarboxylase, LdcI/CadA, together with the inner-membrane lysine-cadaverine antiporter, CadB, provide cells with protection against mild acidic conditions (pH approximately 5). To gain a better understanding of the molecular processes underlying the acid stress response, the X-ray crystal structure of LdcI was determined. The structure revealed that the protein is an oligomer of five dimers that associate to form a decamer. Surprisingly, LdcI was found to co-crystallize with the stringent response effector molecule ppGpp, also known as the alarmone, with 10 ppGpp molecules in the decamer. ppGpp is known to mediate the stringent response, which occurs in response to nutrient deprivation. The alarmone strongly inhibited LdcI enzymatic activity. This inhibition is important for modulating the consumption of lysine in cells during acid stress under nutrient limiting conditions. Hence, our data provide direct evidence for a link between the bacterial acid stress and stringent responses.
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| - | Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase.,Kanjee U, Gutsche I, Alexopoulos E, Zhao B, El Bakkouri M, Thibault G, Liu K, Ramachandran S, Snider J, Pai EF, Houry WA EMBO J. 2011 Jan 28. PMID:21278708<ref>PMID:21278708</ref>
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| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 3q16" style="background-color:#fffaf0;"></div>
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| - | == References ==
| + | |
| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ecoli]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Lysine decarboxylase]] | + | [[Category: Large Structures]] |
| - | [[Category: Bakkouri, M El]] | + | [[Category: El Bakkouri M]] |
| - | [[Category: Houry, W A]] | + | [[Category: Houry WA]] |
| - | [[Category: Pai, E F]] | + | [[Category: Pai EF]] |
| - | [[Category: Aspartate aminotranferase]]
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| - | [[Category: Chey]]
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| - | [[Category: Inducible lysine decarboxylase]]
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| - | [[Category: Lyase]]
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| - | [[Category: Plp]]
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| - | [[Category: Pyridoxal-5-phosphate]]
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