3dfy

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{{Seed}}
 
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[[Image:3dfy.jpg|left|200px]]
 
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==Crystal structure of apo dipeptide epimerase from Thermotoga maritima==
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The line below this paragraph, containing "STRUCTURE_3dfy", creates the "Structure Box" on the page.
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<StructureSection load='3dfy' size='340' side='right'caption='[[3dfy]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3dfy]] is a 16 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=3DFY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DFY FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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{{STRUCTURE_3dfy| PDB=3dfy | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3dfy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dfy OCA], [https://pdbe.org/3dfy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dfy RCSB], [https://www.ebi.ac.uk/pdbsum/3dfy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dfy ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/df/3dfy_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=3dfy ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===Crystal structure of apo dipeptide epimerase from Thermotoga maritima===
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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<ref>PMID:19000819</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3dfy" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_19000819}}, adds the Publication Abstract to the page
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*[[Muconate cycloisomerase|Muconate cycloisomerase]]
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(as it appears on PubMed at http://www.pubmed.gov), where 19000819 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19000819}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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3DFY is a 16 chains structure of sequences from [http://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=3DFY OCA].
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[[Category: Thermotoga maritima MSB8]]
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[[Category: Almo SC]]
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==Reference==
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[[Category: Fedorov AA]]
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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:[http://www.ncbi.nlm.nih.gov/pubmed/19000819 19000819]
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[[Category: Fedorov EV]]
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[[Category: Thermotoga maritima msb8]]
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[[Category: Gerlt JA]]
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[[Category: Almo, S C.]]
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[[Category: Imker HJ]]
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[[Category: Fedorov, A A.]]
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[[Category: Fedorov, E V.]]
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[[Category: Gerlt, J A.]]
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[[Category: Imker, H J.]]
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[[Category: Dipeptide epimerase]]
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[[Category: Enzymatic function]]
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[[Category: Isomerase]]
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[[Category: Thermotoga maritima]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Nov 27 13:36:44 2008''
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Current revision

Crystal structure of apo dipeptide epimerase from Thermotoga maritima

PDB ID 3dfy

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