2dln: Difference between revisions

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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...
 
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[[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''

Latest revision as of 12:18, 14 February 2024

VANCOMYCIN RESISTANCE: STRUCTURE OF D-ALANINE:D-ALANINE LIGASE AT 2.3 ANGSTROMS RESOLUTIONVANCOMYCIN RESISTANCE: STRUCTURE OF D-ALANINE:D-ALANINE LIGASE AT 2.3 ANGSTROMS RESOLUTION

Structural highlights

2dln is a 1 chain structure with sequence from Escherichia coli. The December 2015 RCSB PDB Molecule of the Month feature on Vancomycin by David Goodsell is 10.2210/rcsb_pdb/mom_2015_12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.3Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DDLB_ECOLI Cell wall formation.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2dln, resolution 2.30Å

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