2dln: Difference between revisions

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-[[Image:2dln.jpg|left|200px]]
- {{Structure
+==VANCOMYCIN RESISTANCE: STRUCTURE OF D-ALANINE:D-ALANINE LIGASE AT 2.3 ANGSTROMS RESOLUTION==
-|PDB= 2dln |SIZE=350|CAPTION= <scene name='initialview01'>2dln</scene>, resolution 2.3&Aring;
+<StructureSection load='2dln' size='340' side='right'caption='[[2dln]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ADP:ADENOSINE-5&#39;-DIPHOSPHATE'>ADP</scene> and <scene name='pdbligand=PHY:1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC ACID'>PHY</scene>
+<table><tr><td colspan='2'>[[2dln]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. The December 2015 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Vancomycin''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2015_12 10.2210/rcsb_pdb/mom_2015_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DLN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DLN FirstGlance]. <br>
-|ACTIVITY= [http://en.wikipedia.org/wiki/D-alanine--D-alanine_ligase D-alanine--D-alanine ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.4 6.3.2.4]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHY:1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC+ACID'>PHY</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=2dln FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dln OCA], [https://pdbe.org/2dln PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dln RCSB], [https://www.ebi.ac.uk/pdbsum/2dln PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dln ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DDLB_ECOLI DDLB_ECOLI] Cell wall formation.
+== 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/dl/2dln_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=2dln ConSurf].
+<div style="clear:both"></div>
-'''VANCOMYCIN RESISTANCE: STRUCTURE OF D-ALANINE:D-ALANINE LIGASE AT 2.3 ANGSTROMS RESOLUTION'''
+==See Also==
+*[[D-alanine-D-alanine ligase 3D structures|D-alanine-D-alanine ligase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-The molecular structure of the D-alanine:D-alanine ligase of the ddlB gene of Escherichia coli, co-crystallized with an S,R-methylphosphinate and adenosine triphosphate, was determined by x-ray diffraction to a resolution of 2.3 angstroms. A catalytic mechanism for the ligation of two D-alanine substrates is proposed in which a helix dipole and a hydrogen-bonded triad of tyrosine, serine, and glutamic acid assist binding and deprotonation steps. From sequence comparison, it is proposed that a different triad exists in a recently discovered D-alanine:D-lactate ligase (VanA) present in vancomycin-resistant enterococci. A molecular mechanism for the altered specificity of VanA is suggested.
-==About this Structure==
-DLN is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DLN OCA].
-==Reference==
-Vancomycin resistance: structure of D-alanine:D-alanine ligase at 2.3 A resolution., Fan C, Moews PC, Walsh CT, Knox JR, Science. 1994 Oct 21;266(5184):439-43. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7939684 7939684]
-[[Category: D-alanine--D-alanine ligase]]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Fan, C.]]
+[[Category: RCSB PDB Molecule of the Month]]
-[[Category: Knox, J R.]]
+[[Category: Vancomycin]]
-[[Category: Moews, P C.]]
+[[Category: Fan C]]
-[[Category: ADP]]
+[[Category: Knox JR]]
-[[Category: MG]]
+[[Category: Moews PC]]
-[[Category: PHY]]
-[[Category: ligase(peptidoglycan synthesis)]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 14:56:47 2008''