2hj4: Difference between revisions

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-[[Image:2hj4.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2hj4", creates the "Structure Box" on the page.
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-{{STRUCTURE_2hj4|  PDB=2hj4  |  SCENE=  }}
-'''Crystal structure of Alcaligenes faecalis AADH complex with p-nitrobenzylamine'''
+==Crystal structure of Alcaligenes faecalis AADH complex with p-nitrobenzylamine==
+<StructureSection load='2hj4' size='340' side='right'caption='[[2hj4]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2hj4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HJ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HJ4 FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PNZ:P-NITRO-BENZYLAMINE'>PNZ</scene></td></tr>
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRQ:2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1H-INDOL-3-YL)-PROPIONIC+ACID'>TRQ</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2hj7|2hj7]], [[2hjb|2hjb]], [[2hkm|2hkm]], [[2hkr|2hkr]]</div></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Aralkylamine_dehydrogenase_(azurin) Aralkylamine dehydrogenase (azurin)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.9.2 1.4.9.2] </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=2hj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hj4 OCA], [https://pdbe.org/2hj4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hj4 RCSB], [https://www.ebi.ac.uk/pdbsum/2hj4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hj4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[https://www.uniprot.org/uniprot/AAUA_ALCFA AAUA_ALCFA]] Oxidizes primary aromatic amines and, more slowly, some long-chain aliphatic amines, but not methylamine or ethylamine. Uses azurin as an electron acceptor to transfer electrons from the reduced tryptophylquinone cofactor.<ref>PMID:11495996</ref> <ref>PMID:16279953</ref> <ref>PMID:8188594</ref> <ref>PMID:7876189</ref> <ref>PMID:17087503</ref> <ref>PMID:17005560</ref> <ref>PMID:16614214</ref>  [[https://www.uniprot.org/uniprot/AAUB_ALCFA AAUB_ALCFA]] Oxidizes primary aromatic amines and, more slowly, some long-chain aliphatic amines, but not methylamine or ethylamine. Uses azurin as an electron acceptor to transfer electrons from the reduced tryptophylquinone cofactor.<ref>PMID:11495996</ref> <ref>PMID:16279953</ref> <ref>PMID:8188594</ref> <ref>PMID:16614214</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/hj/2hj4_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=2hj4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Structure-activity correlations have been employed previously in the mechanistic interpretation of TTQ-dependent amine dehydrogenases using a series of para-substituted benzylamines. However, by combining the use of kinetic isotope effects (KIEs) and crystallographic analysis, in conjunction with structure-reactivity correlation studies, we show that para-substituted benzylamines are poor reactivity probes for TTQ-dependent aromatic amine dehydrogenase (AADH). Stopped-flow kinetic studies of the reductive half-reaction, with para-substituted benzylamines and their dideuterated counterparts, demonstrate that C-H or C-D bond breakage is not fully rate limiting (KIEs approximately unity). Contrary to previous reports, Hammett plots exhibit a poor correlation of structure-reactivity data with electronic substituent effects for para-substituted benzylamines and phenylethylamines. Crystallographic studies of enzyme-substrate complexes reveal that the observed structure-reactivity correlations are not attributed to distinct binding modes for para-substituted benzylamines in the active site, although two binding sites for p-nitrobenzylamine are identified. We identify structural rearrangements, prior to the H-transfer step, which are likely to limit the rate of TTQ reduction by benzylamines. This work emphasizes (i) the need for caution when applying structure-activity correlations to enzyme-catalyzed reactions and (ii) the added benefit of using both isotope effects and structural analysis, in conjunction with structure-reactivity relationships, to study chemical steps in enzyme reaction cycles.
-==Overview==
+Isotope effects reveal that para-substituted benzylamines are poor reactivity probes of the quinoprotein mechanism for aromatic amine dehydrogenase.,Hothi P, Roujeinikova A, Khadra KA, Lee M, Cullis P, Leys D, Scrutton NS Biochemistry. 2007 Aug 14;46(32):9250-9. Epub 2007 Jul 18. PMID:17636875<ref>PMID:17636875</ref>
-Structure-activity correlations have been employed previously in the mechanistic interpretation of TTQ-dependent amine dehydrogenases using a series of para-substituted benzylamines. However, by combining the use of kinetic isotope effects (KIEs) and crystallographic analysis, in conjunction with structure-reactivity correlation studies, we show that para-substituted benzylamines are poor reactivity probes for TTQ-dependent aromatic amine dehydrogenase (AADH). Stopped-flow kinetic studies of the reductive half-reaction, with para-substituted benzylamines and their dideuterated counterparts, demonstrate that C-H or C-D bond breakage is not fully rate limiting (KIEs approximately unity). Contrary to previous reports, Hammett plots exhibit a poor correlation of structure-reactivity data with electronic substituent effects for para-substituted benzylamines and phenylethylamines. Crystallographic studies of enzyme-substrate complexes reveal that the observed structure-reactivity correlations are not attributed to distinct binding modes for para-substituted benzylamines in the active site, although two binding sites for p-nitrobenzylamine are identified. We identify structural rearrangements, prior to the H-transfer step, which are likely to limit the rate of TTQ reduction by benzylamines. This work emphasizes (i) the need for caution when applying structure-activity correlations to enzyme-catalyzed reactions and (ii) the added benefit of using both isotope effects and structural analysis, in conjunction with structure-reactivity relationships, to study chemical steps in enzyme reaction cycles.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HJ4 OCA].
+</div>
+<div class="pdbe-citations 2hj4" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Isotope effects reveal that para-substituted benzylamines are poor reactivity probes of the quinoprotein mechanism for aromatic amine dehydrogenase., Hothi P, Roujeinikova A, Khadra KA, Lee M, Cullis P, Leys D, Scrutton NS, Biochemistry. 2007 Aug 14;46(32):9250-9. Epub 2007 Jul 18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17636875 17636875]
+*[[Aromatic amine dehydrogenase 3D structures|Aromatic amine dehydrogenase 3D structures]]
-[[Category: Aralkylamine dehydrogenase]]
+== References ==
-[[Category: Leys, D.]]
+<references/>
-[[Category: Roujeinikova, A.]]
+__TOC__
+</StructureSection>
+[[Category: Alcaligenes faecalis]]
+[[Category: Large Structures]]
+[[Category: Leys, D]]
+[[Category: Roujeinikova, A]]
 [[Category: Kinetic isotope effect]]
 [[Category: Oxidoreductase]]
 [[Category: P-substituted benzylamine]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 06:21:25 2008''