5fkx: Difference between revisions

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'''Unreleased structure'''


The entry 5fkx is ON HOLD  until Paper Publication
==Structure of E.coli inducible lysine decarboxylase at active pH==
<StructureSection load='5fkx' size='340' side='right' caption='[[5fkx]], [[Resolution|resolution]] 6.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5fkx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FKX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FKX FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5fkz|5fkz]], [[5fl2|5fl2]]</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5fkx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fkx OCA], [http://pdbe.org/5fkx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fkx RCSB], [http://www.ebi.ac.uk/pdbsum/5fkx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fkx ProSAT]</span></td></tr>
</table>
== 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.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The inducible lysine decarboxylase LdcI is an important enterobacterial acid stress response enzyme whereas LdcC is its close paralogue thought to play mainly a metabolic role. A unique macromolecular cage formed by two decamers of the Escherichia coli LdcI and five hexamers of the AAA+ ATPase RavA was shown to counteract acid stress under starvation. Previously, we proposed a pseudoatomic model of the LdcI-RavA cage based on its cryo-electron microscopy map and crystal structures of an inactive LdcI decamer and a RavA monomer. We now present cryo-electron microscopy 3D reconstructions of the E. coli LdcI and LdcC, and an improved map of the LdcI bound to the LARA domain of RavA, at pH optimal for their enzymatic activity. Comparison with each other and with available structures uncovers differences between LdcI and LdcC explaining why only the acid stress response enzyme is capable of binding RavA. We identify interdomain movements associated with the pH-dependent enzyme activation and with the RavA binding. Multiple sequence alignment coupled to a phylogenetic analysis reveals that certain enterobacteria exert evolutionary pressure on the lysine decarboxylase towards the cage-like assembly with RavA, implying that this complex may have an important function under particular stress conditions.


Authors: Kandiah, E., Carriel, D., Perard, J., Malet, H., Bacia, M., Liu, K., Chan, S.W.S., Houry, W.A., Ollagnier de Choudens, S., Elsen, S., Gutsche, I.
Structural insights into the Escherichia coli lysine decarboxylases and molecular determinants of interaction with the AAA+ ATPase RavA.,Kandiah E, Carriel D, Perard J, Malet H, Bacia M, Liu K, Chan SW, Houry WA, Ollagnier de Choudens S, Elsen S, Gutsche I Sci Rep. 2016 Apr 15;6:24601. doi: 10.1038/srep24601. PMID:27080013<ref>PMID:27080013</ref>


Description: Structure of E.coli inducible lysine decarboxylase at active pH
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Ollagnier De Choudens, S]]
<div class="pdbe-citations 5fkx" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Lysine decarboxylase]]
[[Category: Bacia, M]]
[[Category: Carriel, D]]
[[Category: Chan, S W.S]]
[[Category: Choudens, S Ollagnier de]]
[[Category: Elsen, S]]
[[Category: Gutsche, I]]
[[Category: Gutsche, I]]
[[Category: Houry, W A]]
[[Category: Kandiah, E]]
[[Category: Kandiah, E]]
[[Category: Bacia, M]]
[[Category: Liu, K]]
[[Category: Malet, H]]
[[Category: Perard, J]]
[[Category: Perard, J]]
[[Category: Elsen, S]]
[[Category: Acid-stress]]
[[Category: Malet, H]]
[[Category: Cage]]
[[Category: Chan, S.W.S]]
[[Category: Lyase]]
[[Category: Carriel, D]]
[[Category: Rava]]
[[Category: Liu, K]]
[[Category: Houry, W.A]]

Revision as of 16:48, 21 September 2016

Structure of E.coli inducible lysine decarboxylase at active pHStructure of E.coli inducible lysine decarboxylase at active pH

Structural highlights

5fkx is a 1 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Activity:Lysine decarboxylase, with EC number 4.1.1.18
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 inducible lysine decarboxylase LdcI is an important enterobacterial acid stress response enzyme whereas LdcC is its close paralogue thought to play mainly a metabolic role. A unique macromolecular cage formed by two decamers of the Escherichia coli LdcI and five hexamers of the AAA+ ATPase RavA was shown to counteract acid stress under starvation. Previously, we proposed a pseudoatomic model of the LdcI-RavA cage based on its cryo-electron microscopy map and crystal structures of an inactive LdcI decamer and a RavA monomer. We now present cryo-electron microscopy 3D reconstructions of the E. coli LdcI and LdcC, and an improved map of the LdcI bound to the LARA domain of RavA, at pH optimal for their enzymatic activity. Comparison with each other and with available structures uncovers differences between LdcI and LdcC explaining why only the acid stress response enzyme is capable of binding RavA. We identify interdomain movements associated with the pH-dependent enzyme activation and with the RavA binding. Multiple sequence alignment coupled to a phylogenetic analysis reveals that certain enterobacteria exert evolutionary pressure on the lysine decarboxylase towards the cage-like assembly with RavA, implying that this complex may have an important function under particular stress conditions.

Structural insights into the Escherichia coli lysine decarboxylases and molecular determinants of interaction with the AAA+ ATPase RavA.,Kandiah E, Carriel D, Perard J, Malet H, Bacia M, Liu K, Chan SW, Houry WA, Ollagnier de Choudens S, Elsen S, Gutsche I Sci Rep. 2016 Apr 15;6:24601. doi: 10.1038/srep24601. PMID:27080013[1]

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

References

  1. ↑ Kandiah E, Carriel D, Perard J, Malet H, Bacia M, Liu K, Chan SW, Houry WA, Ollagnier de Choudens S, Elsen S, Gutsche I. Structural insights into the Escherichia coli lysine decarboxylases and molecular determinants of interaction with the AAA+ ATPase RavA. Sci Rep. 2016 Apr 15;6:24601. doi: 10.1038/srep24601. PMID:27080013 doi:http://dx.doi.org/10.1038/srep24601

5fkx, resolution 6.10Å

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