1jpd: Difference between revisions

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<StructureSection load='1jpd' size='340' side='right'caption='[[1jpd]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
<StructureSection load='1jpd' size='340' side='right'caption='[[1jpd]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1jpd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JPD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JPD FirstGlance]. <br>
<table><tr><td colspan='2'>[[1jpd]] 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=1JPD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JPD FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2muc|2muc]], [[1fhv|1fhv]]</div></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</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=1jpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jpd OCA], [https://pdbe.org/1jpd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jpd RCSB], [https://www.ebi.ac.uk/pdbsum/1jpd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jpd ProSAT]</span></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=1jpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jpd OCA], [https://pdbe.org/1jpd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jpd RCSB], [https://www.ebi.ac.uk/pdbsum/1jpd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jpd ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/AEEP_ECOLI AEEP_ECOLI]] Catalyzes the epimerization of L-Ala-D-Glu to L-Ala-L-Glu and has a role in the recycling of the murein peptide, of which L-Ala-D-Glu is a component. Is also able to catalyze the reverse reaction and the epimerization of all the L-Ala-X dipeptides, except L-Ala-L-Arg, L-Ala-L-Lys and L-Ala-L-Pro. Is also active with L-Gly-L-Glu, L-Phe-L-Glu, and L-Ser-L-Glu, but not with L-Glu-L-Glu, L-Lys-L-Glu, L-Pro-L-Glu, L-Lys-L-Ala, or D-Ala-D-Ala.<ref>PMID:11747447</ref> <ref>PMID:18535144</ref>
[https://www.uniprot.org/uniprot/AEEP_ECOLI AEEP_ECOLI] Catalyzes the epimerization of L-Ala-D-Glu to L-Ala-L-Glu and has a role in the recycling of the murein peptide, of which L-Ala-D-Glu is a component. Is also able to catalyze the reverse reaction and the epimerization of all the L-Ala-X dipeptides, except L-Ala-L-Arg, L-Ala-L-Lys and L-Ala-L-Pro. Is also active with L-Gly-L-Glu, L-Phe-L-Glu, and L-Ser-L-Glu, but not with L-Glu-L-Glu, L-Lys-L-Glu, L-Pro-L-Glu, L-Lys-L-Ala, or D-Ala-D-Ala.<ref>PMID:11747447</ref> <ref>PMID:18535144</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1jpd ConSurf].
</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=1jpd ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The members of the enolase superfamily catalyze different overall reactions, yet share a partial reaction that involves Mg(2+)-assisted enolization of the substrate carboxylate anion. The fate of the resulting enolate intermediate is determined by the active site of each enzyme. Several members of this superfamily have been structurally characterized to permit an understanding of the evolutionary strategy for using a common structural motif to catalyze different overall reactions. In the preceding paper, two new members of the superfamily were identified that catalyze the epimerization of the glutamate residue in L-Ala-D/L-Glu. These enzymes belong to the muconate lactonizing enzyme subgroup of the enolase superfamily, and their sequences are only 31% identical. The structure of YcjG, the epimerase from Escherichia coli, was determined by MAD phasing using both the SeMet-labeled protein and a heavy atom derivative. The structure of YkfB, the epimerase from Bacillus subtilis, was determined by molecular replacement using the muconate lactonizing enzyme as a search model. In this paper, we report the three-dimensional structures of these enzymes and compare them to the structure of o-succinylbenzoate synthase, another member of the muconate lactonizing enzyme subgroup.
Evolution of enzymatic activities in the enolase superfamily: crystal structures of the L-Ala-D/L-Glu epimerases from Escherichia coli and Bacillus subtilis.,Gulick AM, Schmidt DM, Gerlt JA, Rayment I Biochemistry. 2001 Dec 25;40(51):15716-24. PMID:11747448<ref>PMID:11747448</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1jpd" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus coli migula 1895]]
[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Gerlt, J A]]
[[Category: Gerlt JA]]
[[Category: Gulick, A M]]
[[Category: Gulick AM]]
[[Category: Rayment, I]]
[[Category: Rayment I]]
[[Category: Schmidt, D M.Z]]
[[Category: Schmidt DMZ]]
[[Category: Alpha/beta barrel]]
[[Category: Enolase superfamily]]
[[Category: Isomerase]]
[[Category: Muconate lactonizing enzyme subgroup]]
[[Category: Structural genomic]]

Latest revision as of 10:41, 7 February 2024

L-Ala-D/L-Glu EpimeraseL-Ala-D/L-Glu Epimerase

Structural highlights

1jpd is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.6Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AEEP_ECOLI Catalyzes the epimerization of L-Ala-D-Glu to L-Ala-L-Glu and has a role in the recycling of the murein peptide, of which L-Ala-D-Glu is a component. Is also able to catalyze the reverse reaction and the epimerization of all the L-Ala-X dipeptides, except L-Ala-L-Arg, L-Ala-L-Lys and L-Ala-L-Pro. Is also active with L-Gly-L-Glu, L-Phe-L-Glu, and L-Ser-L-Glu, but not with L-Glu-L-Glu, L-Lys-L-Glu, L-Pro-L-Glu, L-Lys-L-Ala, or D-Ala-D-Ala.[1] [2]

Evolutionary Conservation

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

References

  1. ↑ Schmidt DM, Hubbard BK, Gerlt JA. Evolution of enzymatic activities in the enolase superfamily: functional assignment of unknown proteins in Bacillus subtilis and Escherichia coli as L-Ala-D/L-Glu epimerases. Biochemistry. 2001 Dec 25;40(51):15707-15. PMID:11747447
  2. ↑ Park JT, Uehara T. How bacteria consume their own exoskeletons (turnover and recycling of cell wall peptidoglycan). Microbiol Mol Biol Rev. 2008 Jun;72(2):211-27, table of contents. doi:, 10.1128/MMBR.00027-07. PMID:18535144 doi:http://dx.doi.org/10.1128/MMBR.00027-07

1jpd, resolution 2.60Å

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