2y2d: Difference between revisions
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< | ==crystal structure of AmpD holoenzyme== | ||
<StructureSection load='2y2d' size='340' side='right'caption='[[2y2d]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2y2d]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Citrobacter_freundii Citrobacter freundii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Y2D FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=2y2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y2d OCA], [https://pdbe.org/2y2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2y2d RCSB], [https://www.ebi.ac.uk/pdbsum/2y2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2y2d ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/AMPD_CITFR AMPD_CITFR] Involved in both cell wall peptidoglycans recycling and beta-lactamase induction. Specifically cleaves the amide bond between the lactyl group of N-acetylmuramic acid and the alpha-amino group of the L-alanine in degradation products containing an anhydro N-acetylmuramyl moiety. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
AmpD is a cytoplasmic peptidoglycan (PG) amidase involved in bacterial cell-wall recycling and in induction of beta-lactamase, a key enzyme of beta-lactam antibiotic resistance. AmpD belongs to the amidase_2 family that includes zinc-dependent amidases and the peptidoglycan-recognition proteins (PGRPs), highly conserved pattern-recognition molecules of the immune system. Crystal structures of Citrobacter freundii AmpD were solved in this study for the apoenzyme, for the holoenzyme at two different pH values, and for the complex with the reaction products, providing insights into the PG recognition and the catalytic process. These structures are significantly different compared with the previously reported NMR structure for the same protein. The NMR structure does not possess an accessible active site and shows the protein in what is proposed herein as an inactive "closed" conformation. The transition of the protein from this inactive conformation to the active "open" conformation, as seen in the x-ray structures, was studied by targeted molecular dynamics simulations, which revealed large conformational rearrangements (as much as 17 A) in four specific regions representing one-third of the entire protein. It is proposed that the large conformational change that would take the inactive NMR structure to the active x-ray structure represents an unprecedented mechanism for activation of AmpD. Analysis is presented to argue that this activation mechanism might be representative of a regulatory process for other intracellular members of the bacterial amidase_2 family of enzymes. | |||
Crystal Structures of Bacterial Peptidoglycan Amidase AmpD and an Unprecedented Activation Mechanism.,Carrasco-Lopez C, Rojas-Altuve A, Zhang W, Hesek D, Lee M, Barbe S, Andre I, Ferrer P, Silva-Martin N, Castro GR, Martinez-Ripoll M, Mobashery S, Hermoso JA J Biol Chem. 2011 Sep 9;286(36):31714-22. Epub 2011 Jul 20. PMID:21775432<ref>PMID:21775432</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2y2d" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
== | |||
< | |||
[[Category: Citrobacter freundii]] | [[Category: Citrobacter freundii]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Andre | [[Category: Andre I]] | ||
[[Category: Barbe | [[Category: Barbe S]] | ||
[[Category: Carrasco-Lopez | [[Category: Carrasco-Lopez C]] | ||
[[Category: Hermoso | [[Category: Hermoso JA]] | ||
[[Category: Hesek | [[Category: Hesek D]] | ||
[[Category: Lee | [[Category: Lee M]] | ||
[[Category: Martinez-Ripoll | [[Category: Martinez-Ripoll M]] | ||
[[Category: Mobashery | [[Category: Mobashery S]] | ||
[[Category: Rojas-Altuve | [[Category: Rojas-Altuve A]] | ||
[[Category: Silva-Martin | [[Category: Silva-Martin N]] | ||
[[Category: Zhang | [[Category: Zhang W]] | ||
Latest revision as of 13:43, 20 December 2023
crystal structure of AmpD holoenzymecrystal structure of AmpD holoenzyme
Structural highlights
FunctionAMPD_CITFR Involved in both cell wall peptidoglycans recycling and beta-lactamase induction. Specifically cleaves the amide bond between the lactyl group of N-acetylmuramic acid and the alpha-amino group of the L-alanine in degradation products containing an anhydro N-acetylmuramyl moiety. Publication Abstract from PubMedAmpD is a cytoplasmic peptidoglycan (PG) amidase involved in bacterial cell-wall recycling and in induction of beta-lactamase, a key enzyme of beta-lactam antibiotic resistance. AmpD belongs to the amidase_2 family that includes zinc-dependent amidases and the peptidoglycan-recognition proteins (PGRPs), highly conserved pattern-recognition molecules of the immune system. Crystal structures of Citrobacter freundii AmpD were solved in this study for the apoenzyme, for the holoenzyme at two different pH values, and for the complex with the reaction products, providing insights into the PG recognition and the catalytic process. These structures are significantly different compared with the previously reported NMR structure for the same protein. The NMR structure does not possess an accessible active site and shows the protein in what is proposed herein as an inactive "closed" conformation. The transition of the protein from this inactive conformation to the active "open" conformation, as seen in the x-ray structures, was studied by targeted molecular dynamics simulations, which revealed large conformational rearrangements (as much as 17 A) in four specific regions representing one-third of the entire protein. It is proposed that the large conformational change that would take the inactive NMR structure to the active x-ray structure represents an unprecedented mechanism for activation of AmpD. Analysis is presented to argue that this activation mechanism might be representative of a regulatory process for other intracellular members of the bacterial amidase_2 family of enzymes. Crystal Structures of Bacterial Peptidoglycan Amidase AmpD and an Unprecedented Activation Mechanism.,Carrasco-Lopez C, Rojas-Altuve A, Zhang W, Hesek D, Lee M, Barbe S, Andre I, Ferrer P, Silva-Martin N, Castro GR, Martinez-Ripoll M, Mobashery S, Hermoso JA J Biol Chem. 2011 Sep 9;286(36):31714-22. Epub 2011 Jul 20. PMID:21775432[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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