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3des

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Revision as of 12:46, 30 August 2023

Crystal structure of dipeptide epimerase from Thermotoga maritima complexed with L-Ala-L-Phe dipeptide

Structural highlights

3des is a 4 chain structure with sequence from Thermotoga maritima MSB8. 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

AEEP_THEMA Catalyzes the epimerization of L-Ala-D-Glu to L-Ala-L-Glu and has probably a role in the metabolism 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 a broad range of other dipeptides; is most efficient with L-Ala-D/L-Phe, L-Ala-D/L-Tyr, and L-Ala-D/L-His.^[1]

Evolutionary Conservation

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

Publication Abstract from PubMed

We have developed a computational approach to aid the assignment of enzymatic function for uncharacterized proteins that uses homology modeling to predict the structure of the binding site and in silico docking to identify potential substrates. We apply this method to proteins in the functionally diverse enolase superfamily that are homologous to the characterized L-Ala-D/L-Glu epimerase from Bacillus subtilis. In particular, a protein from Thermotoga martima was predicted to have different substrate specificity, which suggests that it has a different, but as yet unknown, biological function. This prediction was experimentally confirmed, resulting in the assignment of epimerase activity for L-Ala-D/L-Phe, L-Ala-D/L-Tyr, and L-Ala-D/L-His, whereas the enzyme is annotated incorrectly in GenBank as muconate cycloisomerase. Subsequently, crystal structures of the enzyme were determined in complex with three substrates, showing close agreement with the computational models and revealing the structural basis for the observed substrate selectivity.

Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening.,Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP Structure. 2008 Nov;16(11):1668-77. PMID:19000819^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP. Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening. Structure. 2008 Nov;16(11):1668-77. PMID:19000819 doi:S0969-2126(08)00371-7
↑ Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP. Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening. Structure. 2008 Nov;16(11):1668-77. PMID:19000819 doi:S0969-2126(08)00371-7

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3des"

@@ Line 3: / Line 3: @@
 <StructureSection load='3des' size='340' side='right'caption='[[3des]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3des]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thema Thema]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DES OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DES FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3des]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DES OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DES FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHE:PHENYLALANINE'>PHE</scene></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]] 2.3&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3deq|3deq]], [[3der|3der]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHE:PHENYLALANINE'>PHE</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TM_0006 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 THEMA])</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=3des FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3des OCA], [https://pdbe.org/3des PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3des RCSB], [https://www.ebi.ac.uk/pdbsum/3des PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3des ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/AEEP_THEMA AEEP_THEMA]] Catalyzes the epimerization of L-Ala-D-Glu to L-Ala-L-Glu and has probably a role in the metabolism 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 a broad range of other dipeptides; is most efficient with L-Ala-D/L-Phe, L-Ala-D/L-Tyr, and L-Ala-D/L-His.<ref>PMID:19000819</ref>
+[https://www.uniprot.org/uniprot/AEEP_THEMA AEEP_THEMA] Catalyzes the epimerization of L-Ala-D-Glu to L-Ala-L-Glu and has probably a role in the metabolism 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 a broad range of other dipeptides; is most efficient with L-Ala-D/L-Phe, L-Ala-D/L-Tyr, and L-Ala-D/L-His.<ref>PMID:19000819</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 38: / Line 37: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Thema]]
+[[Category: Thermotoga maritima MSB8]]
-[[Category: Almo, S C]]
+[[Category: Almo SC]]
-[[Category: Fedorov, A A]]
+[[Category: Fedorov AA]]
-[[Category: Fedorov, E V]]
+[[Category: Fedorov EV]]
-[[Category: Gerlt, J A]]
+[[Category: Gerlt JA]]
-[[Category: Imker, H J]]
+[[Category: Imker HJ]]
-[[Category: Dipeptide epimerase]]
-[[Category: Enzymatic function]]
-[[Category: Isomerase]]
-[[Category: Thermotoga maritima]]

3des

From Proteopedia

Revision as of 12:46, 30 August 2023

Crystal structure of dipeptide epimerase from Thermotoga maritima complexed with L-Ala-L-Phe dipeptide

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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