3n75: Difference between revisions

Latest revision as of 09:09, 6 September 2023

X-ray Crystal Structure of the Escherichia coli Inducible Lysine Decarboxylase LdcI

Structural highlights

3n75 is a 5 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:	G4P, GOL, LLP, P6G
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

LDCI_ECOLI Plays a role in pH homeostasis by consuming protons and neutralizing the acidic by-products of carbohydrate fermentation.

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Kanjee U, Gutsche I, Alexopoulos E, Zhao B, El Bakkouri M, Thibault G, Liu K, Ramachandran S, Snider J, Pai EF, Houry WA. Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase. EMBO J. 2011 Jan 28. PMID:21278708 doi:10.1038/emboj.2011.5

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Kanjee U, Gutsche I, Alexopoulos E, Zhao B, El Bakkouri M, Thibault G, Liu K, Ramachandran S, Snider J, Pai EF, Houry WA. Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase. EMBO J. 2011 Jan 28. PMID:21278708 doi:10.1038/emboj.2011.5

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='3n75' size='340' side='right'caption='[[3n75]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3n75]] is a 5 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=3N75 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N75 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3n75]] 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=3N75 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N75 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G4P:GUANOSINE-5,3-TETRAPHOSPHATE'>G4P</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</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]] 2&#8491;</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>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G4P:GUANOSINE-5,3-TETRAPHOSPHATE'>G4P</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b4131, cadA, JW4092, ldcI, LdcI/CadA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Lysine_decarboxylase Lysine decarboxylase], with EC number [https://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=3n75 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n75 OCA], [https://pdbe.org/3n75 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3n75 RCSB], [https://www.ebi.ac.uk/pdbsum/3n75 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3n75 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[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.
+[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 ==
@@ Line 25: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
+[[Category: Escherichia coli K-12]]
 [[Category: Large Structures]]
-[[Category: Lysine decarboxylase]]
+[[Category: Alexopoulos E]]
-[[Category: Alexopoulos, E]]
+[[Category: Houry WA]]
-[[Category: Houry, W A]]
+[[Category: Kanjee U]]
-[[Category: Kanjee, U]]
+[[Category: Pai EF]]
-[[Category: Pai, E F]]
-[[Category: Acid stress response]]
-[[Category: Lyase]]
-[[Category: Pyridoxal-5'-phosphate dependent decarboxylase]]
-[[Category: Stringent response]]

3n75: Difference between revisions

Latest revision as of 09:09, 6 September 2023

X-ray Crystal Structure of the Escherichia coli Inducible Lysine Decarboxylase LdcI

Structural highlights

Function

Publication Abstract from PubMed

References

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