1d0m: Difference between revisions

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-[[Image:1d0m.jpg|left|200px]]<br /><applet load="1d0m" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1d0m, resolution 2.47&Aring;" />
-'''THE ESCHERICHIA COLI LYTIC TRANSGLYCOSYLASE SLT35 IN COMPLEX WITH BULGECIN A AND (GLCNAC)2'''<br />
-==Overview==
+==THE ESCHERICHIA COLI LYTIC TRANSGLYCOSYLASE SLT35 IN COMPLEX WITH BULGECIN A AND (GLCNAC)2==
-Lytic transglycosylases catalyze the cleavage of the beta-1, 4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) in peptidoglycan with concomitant formation of a 1,6-anhydro bond in the MurNAc residue. To understand the reaction mechanism of Escherichia coli lytic transglycosylase Slt35, three crystal structures have been determined of Slt35 in complex with two different peptidoglycan fragments and with the lytic transglycosylase inhibitor bulgecin A. The complexes define four sugar-binding subsites (-2, -1, +1, and +2) and two peptide-binding sites in a large cleft close to Glu162. The Glu162 side chain is between the -1 and +1 sugar-binding sites, in agreement with a function as catalytic acid/base. The complexes suggest additional contributions to catalysis from Ser216 and Asn339, residues which are conserved among the MltB/Slt35 lytic transglycosylases.
+<StructureSection load='1d0m' size='340' side='right'caption='[[1d0m]], [[Resolution|resolution]] 2.47&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1d0m]] 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=1D0M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D0M FirstGlance]. <br>
-D0M is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=BLG:'>BLG</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D0M OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.47&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BLG:4-O-(4-O-SULFONYL-N-ACETYLGLUCOSAMININYL)-5-METHYLHYDROXY-L-PROLINE-TAURINE'>BLG</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d0m OCA], [https://pdbe.org/1d0m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d0m RCSB], [https://www.ebi.ac.uk/pdbsum/1d0m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d0m ProSAT]</span></td></tr>
-Crystallographic studies of the interactions of Escherichia coli lytic transglycosylase Slt35 with peptidoglycan., van Asselt EJ, Kalk KH, Dijkstra BW, Biochemistry. 2000 Feb 29;39(8):1924-34. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10684641 10684641]
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MLTB_ECOLI MLTB_ECOLI] Murein-degrading enzyme. Catalyzes the cleavage of the glycosidic bonds between N-acetylmuramic acid and N-acetylglucosamine residues in peptidoglycan. May play a role in recycling of muropeptides during cell elongation and/or cell division.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d0/1d0m_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1d0m ConSurf].
+<div style="clear:both"></div>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Asselt, E J.van.]]
+[[Category: Dijkstra BW]]
-[[Category: Dijkstra, B W.]]
+[[Category: Kalk KH]]
-[[Category: Kalk, K H.]]
+[[Category: Van Asselt EJ]]
-[[Category: BLG]]
-[[Category: CA]]
-[[Category: alpha-helical protein with a five stranded anti-parallel beta-sheet]]
-[[Category: ef-hand]]
-[[Category: glycosyl transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:11:45 2008''