1e8c

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:48, 15 November 2023) (edit) (undo)
 
(17 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1e8c.gif|left|200px]]
 
-
{{Structure
+
==Structure of MurE the UDP-N-acetylmuramyl tripeptide synthetase from E. coli==
-
|PDB= 1e8c |SIZE=350|CAPTION= <scene name='initialview01'>1e8c</scene>, resolution 2.00&Aring;
+
<StructureSection load='1e8c' size='340' side='right'caption='[[1e8c]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene> and <scene name='pdbligand=UAG:URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE-D-GLUTAMATE'>UAG</scene>
+
<table><tr><td colspan='2'>[[1e8c]] is a 2 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=1E8C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E8C FirstGlance]. <br>
-
|ACTIVITY=
+
</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&#8491;</td></tr>
-
|GENE= MURE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=API:2,6-DIAMINOPIMELIC+ACID'>API</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=UAG:URIDINE-5-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE-D-GLUTAMATE'>UAG</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=1e8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e8c OCA], [https://pdbe.org/1e8c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e8c RCSB], [https://www.ebi.ac.uk/pdbsum/1e8c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e8c ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/MURE_ECOLI MURE_ECOLI] Catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan. Is also able to use many meso-diaminopimelate analogs as substrates, although much less efficiently, but not L-lysine.<ref>PMID:2269304</ref> <ref>PMID:3905407</ref> <ref>PMID:11124264</ref>
 +
== 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/e8/1e8c_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=1e8c ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
UDP-N-acetylmuramoyl-l-alanyl-d-glutamate:meso-diaminopimelate ligase is a cytoplasmic enzyme that catalyzes the addition of meso-diaminopimelic acid to nucleotide precursor UDP-N-acetylmuramoyl-l-alanyl-d-glutamate in the biosynthesis of bacterial cell-wall peptidoglycan. The crystal structure of the Escherichia coli enzyme in the presence of the final product of the enzymatic reaction, UDP-MurNAc-l-Ala-gamma-d-Glu-meso-A(2)pm, has been solved to 2.0 A resolution. Phase information was obtained by multiwavelength anomalous dispersion using the K shell edge of selenium. The protein consists of three domains, two of which have a topology reminiscent of the equivalent domain found in the already established three-dimensional structure of the UDP-N-acetylmuramoyl-l-alanine: D-glutamate-ligase (MurD) ligase, which catalyzes the immediate previous step of incorporation of d-glutamic acid in the biosynthesis of the peptidoglycan precursor. The refined model reveals the binding site for UDP-MurNAc-l-Ala-gamma-d-Glu-meso-A(2)pm, and comparison with the six known MurD structures allowed the identification of residues involved in the enzymatic mechanism. Interestingly, during refinement, an excess of electron density was observed, leading to the conclusion that, as in MurD, a carbamylated lysine residue is present in the active site. In addition, the structural determinant responsible for the selection of the amino acid to be added to the nucleotide precursor was identified.
-
'''STRUCTURE OF MURE THE UDP-N-ACETYLMURAMYL TRIPEPTIDE SYNTHETASE FROM E. COLI'''
+
Crystal structure of UDP-N-acetylmuramoyl-L-alanyl-D-glutamate: meso-diaminopimelate ligase from Escherichia coli.,Gordon E, Flouret B, Chantalat L, van Heijenoort J, Mengin-Lecreulx D, Dideberg O J Biol Chem. 2001 Apr 6;276(14):10999-1006. Epub 2000 Dec 20. PMID:11124264<ref>PMID:11124264</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 1e8c" style="background-color:#fffaf0;"></div>
-
==Overview==
+
==See Also==
-
UDP-N-acetylmuramoyl-l-alanyl-d-glutamate:meso-diaminopimelate ligase is a cytoplasmic enzyme that catalyzes the addition of meso-diaminopimelic acid to nucleotide precursor UDP-N-acetylmuramoyl-l-alanyl-d-glutamate in the biosynthesis of bacterial cell-wall peptidoglycan. The crystal structure of the Escherichia coli enzyme in the presence of the final product of the enzymatic reaction, UDP-MurNAc-l-Ala-gamma-d-Glu-meso-A(2)pm, has been solved to 2.0 A resolution. Phase information was obtained by multiwavelength anomalous dispersion using the K shell edge of selenium. The protein consists of three domains, two of which have a topology reminiscent of the equivalent domain found in the already established three-dimensional structure of the UDP-N-acetylmuramoyl-l-alanine: D-glutamate-ligase (MurD) ligase, which catalyzes the immediate previous step of incorporation of d-glutamic acid in the biosynthesis of the peptidoglycan precursor. The refined model reveals the binding site for UDP-MurNAc-l-Ala-gamma-d-Glu-meso-A(2)pm, and comparison with the six known MurD structures allowed the identification of residues involved in the enzymatic mechanism. Interestingly, during refinement, an excess of electron density was observed, leading to the conclusion that, as in MurD, a carbamylated lysine residue is present in the active site. In addition, the structural determinant responsible for the selection of the amino acid to be added to the nucleotide precursor was identified.
+
*[[Mur ligase|Mur ligase]]
-
 
+
== References ==
-
==About this Structure==
+
<references/>
-
1E8C 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=1E8C OCA].
+
__TOC__
-
 
+
</StructureSection>
-
==Reference==
+
-
Crystal structure of UDP-N-acetylmuramoyl-L-alanyl-D-glutamate: meso-diaminopimelate ligase from Escherichia coli., Gordon E, Flouret B, Chantalat L, van Heijenoort J, Mengin-Lecreulx D, Dideberg O, J Biol Chem. 2001 Apr 6;276(14):10999-1006. Epub 2000 Dec 20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11124264 11124264]
+
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Chantala, L.]]
+
[[Category: Chantala L]]
-
[[Category: Dideberg, O.]]
+
[[Category: Dideberg O]]
-
[[Category: Gordon, E J.]]
+
[[Category: Gordon EJ]]
-
[[Category: CL]]
+
-
[[Category: UAG]]
+
-
[[Category: ligase]]
+
-
[[Category: peptidoglycan biosynthesis]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:51:34 2008''
+

Current revision

Structure of MurE the UDP-N-acetylmuramyl tripeptide synthetase from E. coli

PDB ID 1e8c

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1e8c"
Personal tools