4bin: Difference between revisions

Latest revision as of 11:52, 20 December 2023

Crystal structure of the E. coli N-acetylmuramoyl-L-alanine amidase AmiC

Structural highlights

4bin is a 1 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 2.49Å
Ligands:	NA, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AMIC_ECOLI Cell-wall hydrolase involved in septum cleavage during cell division. Can also act as powerful autolysin in the presence of murein synthesis inhibitors.^[1] ^[2]

Publication Abstract from PubMed

Binary fission is the ultimate step of the prokaryotic cell cycle. In Gram-negative bacteria like Escherichia coli, this step implies the invagination of three biological layers (cytoplasmic membrane, peptidoglycan and outer membrane), biosynthesis of the new poles and eventually, daughter cells separation. The latter requires the coordinated action of the N-acetylmuramyl-L-alanine amidases AmiA/B/C and their LytM activators EnvC and NlpD to cleave the septal peptidoglycan. We present here the 2.5 A crystal structure of AmiC which includes the first report of an AMIN domain structure, a beta-sandwich of two symmetrical four-stranded beta-sheets exposing highly conserved motifs on the two outer faces. We show that this N-terminal domain, involved in the localization of AmiC at the division site, is a new peptidoglycan-binding domain. The C-terminal catalytic domain shows an auto-inhibitory alpha helix obstructing the active site. AmiC lacking this helix exhibits by itself an activity comparable to that of the wild type AmiC activated by NlpD. We also demonstrate the interaction between AmiC and NlpD by microscale thermophoresis and confirm the importance of the active site blocking alpha helix in the regulation of the amidase activity.

The crystal structure of the cell division amidase AmiC reveals the fold of the AMIN domain, a new peptidoglycan binding domain.,Rocaboy M, Herman R, Sauvage E, Remaut H, Moonens K, Terrak M, Charlier P, Kerff F Mol Microbiol. 2013 Aug 8. doi: 10.1111/mmi.12361. PMID:23927005^[3]

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

References

↑ Heidrich C, Templin MF, Ursinus A, Merdanovic M, Berger J, Schwarz H, de Pedro MA, Holtje JV. Involvement of N-acetylmuramyl-L-alanine amidases in cell separation and antibiotic-induced autolysis of Escherichia coli. Mol Microbiol. 2001 Jul;41(1):167-78. PMID:11454209
↑ Uehara T, Park JT. Growth of Escherichia coli: significance of peptidoglycan degradation during elongation and septation. J Bacteriol. 2008 Jun;190(11):3914-22. doi: 10.1128/JB.00207-08. Epub 2008 Apr 4. PMID:18390656 doi:10.1128/JB.00207-08
↑ Rocaboy M, Herman R, Sauvage E, Remaut H, Moonens K, Terrak M, Charlier P, Kerff F. The crystal structure of the cell division amidase AmiC reveals the fold of the AMIN domain, a new peptidoglycan binding domain. Mol Microbiol. 2013 Aug 8. doi: 10.1111/mmi.12361. PMID:23927005 doi:10.1111/mmi.12361

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Heidrich C, Templin MF, Ursinus A, Merdanovic M, Berger J, Schwarz H, de Pedro MA, Holtje JV. Involvement of N-acetylmuramyl-L-alanine amidases in cell separation and antibiotic-induced autolysis of Escherichia coli. Mol Microbiol. 2001 Jul;41(1):167-78. PMID:11454209

[2] Uehara T, Park JT. Growth of Escherichia coli: significance of peptidoglycan degradation during elongation and septation. J Bacteriol. 2008 Jun;190(11):3914-22. doi: 10.1128/JB.00207-08. Epub 2008 Apr 4. PMID:18390656 doi:10.1128/JB.00207-08

[3] Rocaboy M, Herman R, Sauvage E, Remaut H, Moonens K, Terrak M, Charlier P, Kerff F. The crystal structure of the cell division amidase AmiC reveals the fold of the AMIN domain, a new peptidoglycan binding domain. Mol Microbiol. 2013 Aug 8. doi: 10.1111/mmi.12361. PMID:23927005 doi:10.1111/mmi.12361

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='4bin' size='340' side='right'caption='[[4bin]], [[Resolution|resolution]] 2.49&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4bin]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BIN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BIN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4bin]] is a 1 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=4BIN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BIN FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.49&#8491;</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <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=4bin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bin OCA], [https://pdbe.org/4bin PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4bin RCSB], [https://www.ebi.ac.uk/pdbsum/4bin PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4bin ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/AMIC_ECOLI AMIC_ECOLI]] Cell-wall hydrolase involved in septum cleavage during cell division. Can also act as powerful autolysin in the presence of murein synthesis inhibitors.<ref>PMID:11454209</ref> <ref>PMID:18390656</ref>
+[https://www.uniprot.org/uniprot/AMIC_ECOLI AMIC_ECOLI] Cell-wall hydrolase involved in septum cleavage during cell division. Can also act as powerful autolysin in the presence of murein synthesis inhibitors.<ref>PMID:11454209</ref> <ref>PMID:18390656</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Escherichia coli]]
+[[Category: Escherichia coli K-12]]
 [[Category: Large Structures]]
-[[Category: N-acetylmuramoyl-L-alanine amidase]]
+[[Category: Charlier P]]
-[[Category: Charlier, P]]
+[[Category: Herman R]]
-[[Category: Herman, R]]
+[[Category: Kerff F]]
-[[Category: Kerff, F]]
+[[Category: Rocaboy M]]
-[[Category: Rocaboy, M]]
+[[Category: Sauvage E]]
-[[Category: Sauvage, E]]
-[[Category: Bacterial division]]
-[[Category: Hydrolase]]

4bin: Difference between revisions

Latest revision as of 11:52, 20 December 2023

Crystal structure of the E. coli N-acetylmuramoyl-L-alanine amidase AmiC

Structural highlights

Function

Publication Abstract from PubMed

References

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