3ik4: Difference between revisions
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< | ==CRYSTAL STRUCTURE OF mandelate racemase/muconate lactonizing protein from Herpetosiphon aurantiacus== | ||
<StructureSection load='3ik4' size='340' side='right'caption='[[3ik4]], [[Resolution|resolution]] 2.10Å' scene=''> | |||
You may | == Structural highlights == | ||
or the | <table><tr><td colspan='2'>[[3ik4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Herpetosiphon_aurantiacus_DSM_785 Herpetosiphon aurantiacus DSM 785]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IK4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IK4 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]] 2.1Å</td></tr> | |||
- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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=3ik4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ik4 OCA], [https://pdbe.org/3ik4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ik4 RCSB], [https://www.ebi.ac.uk/pdbsum/3ik4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ik4 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/AREP_HERA2 AREP_HERA2] Has epimerase activity with a variety of hydrophobic dipeptides (in vitro). Enzyme activity is highest with L-Phe-L-Tyr, but is still relatively low, suggesting that L-Phe-L-Tyr is not the physiological substrate.<ref>PMID:22392983</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/ik/3ik4_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=3ik4 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The rapid advance in genome sequencing presents substantial challenges for protein functional assignment, with half or more of new protein sequences inferred from these genomes having uncertain assignments. The assignment of enzyme function in functionally diverse superfamilies represents a particular challenge, which we address through a combination of computational predictions, enzymology, and structural biology. Here we describe the results of a focused investigation of a group of enzymes in the enolase superfamily that are involved in epimerizing dipeptides. The first members of this group to be functionally characterized were Ala-Glu epimerases in Eschericiha coli and Bacillus subtilis, based on the operon context and enzymological studies; these enzymes are presumed to be involved in peptidoglycan recycling. We have subsequently studied more than 65 related enzymes by computational methods, including homology modeling and metabolite docking, which suggested that many would have divergent specificities;, i.e., they are likely to have different (unknown) biological roles. In addition to the Ala-Phe epimerase specificity reported previously, we describe the prediction and experimental verification of: (i) a new group of presumed Ala-Glu epimerases; (ii) several enzymes with specificity for hydrophobic dipeptides, including one from Cytophaga hutchinsonii that epimerizes D-Ala-D-Ala; and (iii) a small group of enzymes that epimerize cationic dipeptides. Crystal structures for certain of these enzymes further elucidate the structural basis of the specificities. The results highlight the potential of computational methods to guide experimental characterization of enzymes in an automated, large-scale fashion. | |||
Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.,Lukk T, Sakai A, Kalyanaraman C, Brown SD, Imker HJ, Song L, Fedorov AA, Fedorov EV, Toro R, Hillerich B, Seidel R, Patskovsky Y, Vetting MW, Nair SK, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP Proc Natl Acad Sci U S A. 2012 Mar 13;109(11):4122-7. Epub 2012 Mar 5. PMID:22392983<ref>PMID:22392983</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3ik4" style="background-color:#fffaf0;"></div> | |||
== | ==See Also== | ||
*[[Mandelate racemase|Mandelate racemase]] | |||
[[Category: | *[[Mandelate racemase/muconate lactonizing enzyme 3D structures|Mandelate racemase/muconate lactonizing enzyme 3D structures]] | ||
[[Category: Almo | == References == | ||
[[Category: Burley | <references/> | ||
[[Category: Dickey | __TOC__ | ||
[[Category: Gerlt | </StructureSection> | ||
[[Category: Iizuka | [[Category: Herpetosiphon aurantiacus DSM 785]] | ||
[[Category: Large Structures]] | |||
[[Category: Patskovsky | [[Category: Almo SC]] | ||
[[Category: Sauder | [[Category: Burley SK]] | ||
[[Category: Toro | [[Category: Dickey M]] | ||
[[Category: Gerlt JA]] | |||
[[Category: Iizuka M]] | |||
[[Category: Patskovsky Y]] | |||
[[Category: Sauder JM]] | |||
[[Category: Toro R]] | |||
Latest revision as of 10:52, 6 September 2023
CRYSTAL STRUCTURE OF mandelate racemase/muconate lactonizing protein from Herpetosiphon aurantiacusCRYSTAL STRUCTURE OF mandelate racemase/muconate lactonizing protein from Herpetosiphon aurantiacus
Structural highlights
FunctionAREP_HERA2 Has epimerase activity with a variety of hydrophobic dipeptides (in vitro). Enzyme activity is highest with L-Phe-L-Tyr, but is still relatively low, suggesting that L-Phe-L-Tyr is not the physiological substrate.[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 PubMedThe rapid advance in genome sequencing presents substantial challenges for protein functional assignment, with half or more of new protein sequences inferred from these genomes having uncertain assignments. The assignment of enzyme function in functionally diverse superfamilies represents a particular challenge, which we address through a combination of computational predictions, enzymology, and structural biology. Here we describe the results of a focused investigation of a group of enzymes in the enolase superfamily that are involved in epimerizing dipeptides. The first members of this group to be functionally characterized were Ala-Glu epimerases in Eschericiha coli and Bacillus subtilis, based on the operon context and enzymological studies; these enzymes are presumed to be involved in peptidoglycan recycling. We have subsequently studied more than 65 related enzymes by computational methods, including homology modeling and metabolite docking, which suggested that many would have divergent specificities;, i.e., they are likely to have different (unknown) biological roles. In addition to the Ala-Phe epimerase specificity reported previously, we describe the prediction and experimental verification of: (i) a new group of presumed Ala-Glu epimerases; (ii) several enzymes with specificity for hydrophobic dipeptides, including one from Cytophaga hutchinsonii that epimerizes D-Ala-D-Ala; and (iii) a small group of enzymes that epimerize cationic dipeptides. Crystal structures for certain of these enzymes further elucidate the structural basis of the specificities. The results highlight the potential of computational methods to guide experimental characterization of enzymes in an automated, large-scale fashion. Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.,Lukk T, Sakai A, Kalyanaraman C, Brown SD, Imker HJ, Song L, Fedorov AA, Fedorov EV, Toro R, Hillerich B, Seidel R, Patskovsky Y, Vetting MW, Nair SK, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP Proc Natl Acad Sci U S A. 2012 Mar 13;109(11):4122-7. Epub 2012 Mar 5. PMID:22392983[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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