|
|
| (3 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | + | |
| | ==Crystal structure of ethanolamine ammonia-lyase from escherichia coli complexed with CN-CBL and (R)-2-amino-1-propanol== | | ==Crystal structure of ethanolamine ammonia-lyase from escherichia coli complexed with CN-CBL and (R)-2-amino-1-propanol== |
| - | <StructureSection load='3any' size='340' side='right' caption='[[3any]], [[Resolution|resolution]] 2.10Å' scene=''> | + | <StructureSection load='3any' size='340' side='right'caption='[[3any]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3any]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ANY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ANY FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3any]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ANY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ANY FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2A3:(2R)-2-AMINOPROPAN-1-OL'>2A3</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</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]] 2.1Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3abo|3abo]], [[3abq|3abq]], [[3abr|3abr]], [[3abs|3abs]], [[3ao0|3ao0]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2A3:(2R)-2-AMINOPROPAN-1-OL'>2A3</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">eutB, b2441, JW2434 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12]), eutC, b2440, JW2433 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</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=3any FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3any OCA], [https://pdbe.org/3any PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3any RCSB], [https://www.ebi.ac.uk/pdbsum/3any PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3any ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ethanolamine_ammonia-lyase Ethanolamine ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.7 4.3.1.7] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3any FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3any OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3any RCSB], [http://www.ebi.ac.uk/pdbsum/3any PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/EUTB_ECOLI EUTB_ECOLI] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 17: |
Line 18: |
| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 3any" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Escherichia coli k-12]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Ethanolamine ammonia-lyase]] | + | [[Category: Large Structures]] |
| - | [[Category: Shibata, N.]] | + | [[Category: Shibata N]] |
| - | [[Category: Cobalamin]]
| + | |
| - | [[Category: Cobalt]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Tim barrel]]
| + | |
| Structural highlights
Function
EUTB_ECOLI
Publication Abstract from PubMed
Coenzyme B(12)-dependent ethanolamine ammonia-lyase acts on both enantiomers of the substrate 2-amino-1-propanol [Diziol, P., et al. (1980) Eur. J. Biochem. 106, 211-224]. To rationalize this apparent lack of stereospecificity and the enantiomer-specific stereochemical courses of the deamination, we analyzed the X-ray structures of enantiomer-bound forms of the enzyme-cyanocobalamin complex. The lower affinity for the (R)-enantiomer may be due to the conformational change of the Valalpha326 side chain of the enzyme. In a manner consistent with the reported experimental results, we can predict that the pro-S hydrogen atom on C1 is abstracted by the adenosyl radical from both enantiomeric substrates, because it is the nearest one in both enantiomer-bound forms. We also predicted that the NH(2) group migrates from C2 to C1 by a suprafacial shift, with inversion of configuration at C1 for both enantiomeric substrates, although the absolute configuration of the 1-amino-1-propanol intermediate is not yet known. Reported labeling experiments demonstrate that (R)-2-amino-1-propanol is deaminated by the enzyme with inversion of configuration at C2, whereas the (S)-enantiomer is deaminated with retention. By taking these results into consideration, we can predict the rotameric radical intermediate from the (S)-enantiomer undergoes flipping to the rotamer from the (R)-enantiomer before the hydrogen back-abstraction. This suggests the preference of the enzyme active site for the rotamer from the (R)-enantiomer in equilibration. This preference might be explained in terms of the steric repulsion of the (S)-enantiomer-derived product radical at C3 with the Phealpha329 and Leualpha402 residues.
How coenzyme B12-dependent ethanolamine ammonia-lyase deals with both enantiomers of 2-amino-1-propanol as substrates: structure-based rationalization.,Shibata N, Higuchi Y, Toraya T Biochemistry. 2011 Feb 1;50(4):591-8. Epub 2010 Dec 30. PMID:21142024[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Shibata N, Higuchi Y, Toraya T. How coenzyme B12-dependent ethanolamine ammonia-lyase deals with both enantiomers of 2-amino-1-propanol as substrates: structure-based rationalization. Biochemistry. 2011 Feb 1;50(4):591-8. Epub 2010 Dec 30. PMID:21142024 doi:10.1021/bi101696h
|
