2y2b

From Proteopedia

(Difference between revisions)

Revision as of 07:27, 3 November 2022

crystal structure of AmpD in complex with reaction products

Structural highlights

2y2b is a 3 chain structure with sequence from Citrobacter freundii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.

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^[1]

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

References

↑ 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. Crystal Structures of Bacterial Peptidoglycan Amidase AmpD and an Unprecedented Activation Mechanism. J Biol Chem. 2011 Sep 9;286(36):31714-22. Epub 2011 Jul 20. PMID:21775432 doi:10.1074/jbc.M111.264366

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2y2b"

@@ Line 3: / Line 3: @@
 <StructureSection load='2y2b' size='340' side='right'caption='[[2y2b]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2y2b]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacterium_freundii"_braak_1928 "bacterium freundii" braak 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y2B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Y2B FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2y2b]] 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=2Y2B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Y2B FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AH0:2-(2-ACETYLAMINO-4-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCT-3-YLOXY)-PROPIONIC+ACID'>AH0</scene>, <scene name='pdbligand=MHI:L-ALA-GAMMA-D-GLU-MESO-DIAMINOPIMELIC+ACID'>MHI</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1j3g|1j3g]], [[2y2c|2y2c]], [[2y2d|2y2d]], [[2y2e|2y2e]], [[2y28|2y28]]</div></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/N-acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.28 3.5.1.28] </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=2y2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y2b OCA], [https://pdbe.org/2y2b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2y2b RCSB], [https://www.ebi.ac.uk/pdbsum/2y2b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2y2b 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.
+[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 ==
@@ Line 27: / Line 25: @@
 __TOC__
 </StructureSection>
-[[Category: Bacterium freundii braak 1928]]
+[[Category: Citrobacter freundii]]
 [[Category: Large Structures]]
-[[Category: N-acetylmuramoyl-L-alanine amidase]]
+[[Category: Andre I]]
-[[Category: Andre, I]]
+[[Category: Barbe S]]
-[[Category: Barbe, S]]
+[[Category: Carrasco-Lopez C]]
-[[Category: Carrasco-Lopez, C]]
+[[Category: Hermoso JA]]
-[[Category: Hermoso, J A]]
+[[Category: Hesek D]]
-[[Category: Hesek, D]]
+[[Category: Lee M]]
-[[Category: Lee, M]]
+[[Category: Martinez-Ripoll M]]
-[[Category: Martinez-Ripoll, M]]
+[[Category: Mobashery S]]
-[[Category: Mobashery, S]]
+[[Category: Rojas-Altuve A]]
-[[Category: Rojas-Altuve, A]]
+[[Category: Silva-Martin N]]
-[[Category: Silva-Martin, N]]
+[[Category: Zhang W]]
-[[Category: Zhang, W]]
-[[Category: Activation mechanism]]
-[[Category: Amidase_2 family]]
-[[Category: Hydrolase]]
-[[Category: Peptidoglycan amidase]]

2y2b

From Proteopedia

Revision as of 07:27, 3 November 2022

crystal structure of AmpD in complex with reaction products

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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