1xrs: Difference between revisions
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==Crystal structure of Lysine 5,6-Aminomutase in complex with PLP, cobalamin, and 5'-deoxyadenosine== | ==Crystal structure of Lysine 5,6-Aminomutase in complex with PLP, cobalamin, and 5'-deoxyadenosine== | ||
<StructureSection load='1xrs' size='340' side='right' caption='[[1xrs]], [[Resolution|resolution]] 2.80Å' scene=''> | <StructureSection load='1xrs' size='340' side='right'caption='[[1xrs]], [[Resolution|resolution]] 2.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1xrs]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12662 Atcc 12662]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XRS OCA]. For a <b>guided tour on the structure components</b> use [http:// | <table><tr><td colspan='2'>[[1xrs]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12662 Atcc 12662]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XRS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1XRS FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">KamDE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1511 ATCC 12662])</td></tr> | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">KamDE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1511 ATCC 12662])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lysine_5,6-aminomutase Beta-lysine 5,6-aminomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.3.3 5.4.3.3] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lysine_5,6-aminomutase Beta-lysine 5,6-aminomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.3.3 5.4.3.3] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http:// | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1xrs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xrs OCA], [http://pdbe.org/1xrs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xrs RCSB], [http://www.ebi.ac.uk/pdbsum/1xrs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xrs ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
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Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xr/1xrs_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xr/1xrs_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
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==See Also== | ==See Also== | ||
*[[Aminomutase|Aminomutase]] | *[[Aminomutase 3D structures|Aminomutase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
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[[Category: Atcc 12662]] | [[Category: Atcc 12662]] | ||
[[Category: Beta-lysine 5,6-aminomutase]] | [[Category: Beta-lysine 5,6-aminomutase]] | ||
[[Category: Large Structures]] | |||
[[Category: Behshad, E]] | [[Category: Behshad, E]] | ||
[[Category: Berkovitch, F]] | [[Category: Berkovitch, F]] | ||
Revision as of 13:17, 6 January 2021
Crystal structure of Lysine 5,6-Aminomutase in complex with PLP, cobalamin, and 5'-deoxyadenosineCrystal structure of Lysine 5,6-Aminomutase in complex with PLP, cobalamin, and 5'-deoxyadenosine
Structural highlights
Function[KAMDD_CLOSD] Catalyzes the 1,2-migration of the D-lysine epsilon amino group to the delta carbon with concomitant reverse migration of a hydrogen atom to produce 2,5-diaminohexanoic acid.[1] [KAMED_CLOSD] Catalyzes the 1,2-migration of the D-lysine epsilon amino group to the delta carbon with concomitant reverse migration of a hydrogen atom to produce 2,5-diaminohexanoic acid.[2] 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 PubMedLysine 5,6-aminomutase is an adenosylcobalamin and pyridoxal-5'-phosphate-dependent enzyme that catalyzes a 1,2 rearrangement of the terminal amino group of dl-lysine and of l-beta-lysine. We have solved the x-ray structure of a substrate-free form of lysine-5,6-aminomutase from Clostridium sticklandii. In this structure, a Rossmann domain covalently binds pyridoxal-5'-phosphate by means of lysine 144 and positions it into the putative active site of a neighboring triosephosphate isomerase barrel domain, while simultaneously positioning the other cofactor, adenosylcobalamin, approximately 25 A from the active site. In this mode of pyridoxal-5'-phosphate binding, the cofactor acts as an anchor, tethering the separate polypeptide chain of the Rossmann domain to the triosephosphate isomerase barrel domain. Upon substrate binding and transaldimination of the lysine-144 linkage, the Rossmann domain would be free to rotate and bring adenosylcobalamin, pyridoxal-5'-phosphate, and substrate into proximity. Thus, the structure embodies a locking mechanism to keep the adenosylcobalamin out of the active site and prevent radical generation in the absence of substrate. A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase.,Berkovitch F, Behshad E, Tang KH, Enns EA, Frey PA, Drennan CL Proc Natl Acad Sci U S A. 2004 Nov 9;101(45):15870-5. Epub 2004 Oct 28. PMID:15514022[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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