2dln: Difference between revisions

From Proteopedia
Jump to navigationJump to search
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
New page: left|200px<br /><applet load="2dln" size="450" color="white" frame="true" align="right" spinBox="true" caption="2dln, resolution 2.3Å" /> '''VANCOMYCIN RESISTANCE...
 
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
 
(15 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2dln.jpg|left|200px]]<br /><applet load="2dln" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2dln, resolution 2.3&Aring;" />
'''VANCOMYCIN RESISTANCE: STRUCTURE OF D-ALANINE:D-ALANINE LIGASE AT 2.3 ANGSTROMS RESOLUTION'''<br />


==Overview==
==VANCOMYCIN RESISTANCE: STRUCTURE OF D-ALANINE:D-ALANINE LIGASE AT 2.3 ANGSTROMS RESOLUTION==
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.
<StructureSection load='2dln' size='340' side='right'caption='[[2dln]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
<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>
</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>
<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>


==About this Structure==
==See Also==
2DLN 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 MG, ADP and PHY as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2DLN OCA].
*[[D-alanine-D-alanine ligase 3D structures|D-alanine-D-alanine ligase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=7939684 7939684]
[[Category: D-alanine--D-alanine ligase]]
[[Category: Escherichia coli]]
[[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://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 09:39:28 2007''
Retrieved from "https://proteopedia.org/2dln"