|
|
| Line 3: |
Line 3: |
| | <StructureSection load='4xbj' size='340' side='right'caption='[[4xbj]], [[Resolution|resolution]] 2.25Å' scene=''> | | <StructureSection load='4xbj' size='340' side='right'caption='[[4xbj]], [[Resolution|resolution]] 2.25Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4xbj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XBJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XBJ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4xbj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XBJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XBJ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IN5:{1-[(3-HYDROXY-METHYL-5-PHOSPHONOOXY-METHYL-PYRIDIN-4-YLMETHYL)-AMINO]-ETHYL}-PHOSPHONIC+ACID'>IN5</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.25Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4wr3|4wr3]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IN5:{1-[(3-HYDROXY-METHYL-5-PHOSPHONOOXY-METHYL-PYRIDIN-4-YLMETHYL)-AMINO]-ETHYL}-PHOSPHONIC+ACID'>IN5</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">alr ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Alanine_racemase Alanine racemase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.1 5.1.1.1] </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=4xbj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xbj OCA], [https://pdbe.org/4xbj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xbj RCSB], [https://www.ebi.ac.uk/pdbsum/4xbj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xbj ProSAT]</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=4xbj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xbj OCA], [https://pdbe.org/4xbj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xbj RCSB], [https://www.ebi.ac.uk/pdbsum/4xbj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xbj ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/ALR1_ECOLI ALR1_ECOLI]] Catalyzes the interconversion of L-alanine and D-alanine. Provides the D-alanine required for cell wall biosynthesis.<ref>PMID:18434499</ref>
| + | [https://www.uniprot.org/uniprot/ALR1_ECOLI ALR1_ECOLI] Catalyzes the interconversion of L-alanine and D-alanine. Provides the D-alanine required for cell wall biosynthesis.<ref>PMID:18434499</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 28: |
Line 26: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| - | [[Category: Alanine racemase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Patrick, W M]] | + | [[Category: Patrick WM]] |
| - | [[Category: Squire, C J]] | + | [[Category: Squire CJ]] |
| - | [[Category: Yosaatmadja, Y]] | + | [[Category: Yosaatmadja Y]] |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Isomerase-isomerase inhibitor complex]]
| + | |
| Structural highlights
Function
ALR1_ECOLI Catalyzes the interconversion of L-alanine and D-alanine. Provides the D-alanine required for cell wall biosynthesis.[1]
Publication Abstract from PubMed
Enzymes that utilize the cofactor pyridoxal 5'-phosphate play essential roles in amino acid metabolism in all organisms. The cofactor is used by proteins that adopt at least five different folds, which raises questions about the evolutionary processes that might explain the observed distribution of functions among folds. In this study, we show that a representative of fold type III, the Escherichia coli alanine racemase (ALR), is a promiscuous cystathionine beta-lyase (CBL). Furthermore, E. coli CBL (fold type I) is a promiscuous alanine racemase. A single round of error-prone PCR and selection yielded variant ALR(Y274F), which catalyzes cystathionine beta-elimination with a near-native Michaelis constant (Km = 3.3 mm) but a poor turnover number (kcat approximately 10 h(-1)). In contrast, directed evolution also yielded CBL(P113S), which catalyzes l-alanine racemization with a poor Km (58 mm) but a high kcat (22 s(-1)). The structures of both variants were solved in the presence and absence of the l-alanine analogue, (R)-1-aminoethylphosphonic acid. As expected, the ALR active site was enlarged by the Y274F substitution, allowing better access for cystathionine. More surprisingly, the favorable kinetic parameters of CBL(P113S) appear to result from optimizing the pKa of Tyr-111, which acts as the catalytic acid during l-alanine racemization. Our data emphasize the short mutational routes between the functions of pyridoxal 5'-phosphate-dependent enzymes, regardless of whether or not they share the same fold. Thus, they confound the prevailing model of enzyme evolution, which predicts that overlapping patterns of promiscuity result from sharing a common multifunctional ancestor.
Mechanistic and Evolutionary Insights from the Reciprocal Promiscuity of Two Pyridoxal Phosphate-dependent Enzymes.,Soo VW, Yosaatmadja Y, Squire CJ, Patrick WM J Biol Chem. 2016 Sep 16;291(38):19873-87. doi: 10.1074/jbc.M116.739557. Epub, 2016 Jul 29. PMID:27474741[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Wu D, Hu T, Zhang L, Chen J, Du J, Ding J, Jiang H, Shen X. Residues Asp164 and Glu165 at the substrate entryway function potently in substrate orientation of alanine racemase from E. coli: Enzymatic characterization with crystal structure analysis. Protein Sci. 2008 Jun;17(6):1066-76. Epub 2008 Apr 23. PMID:18434499 doi:10.1110/ps.083495908
- ↑ Soo VW, Yosaatmadja Y, Squire CJ, Patrick WM. Mechanistic and Evolutionary Insights from the Reciprocal Promiscuity of Two Pyridoxal Phosphate-dependent Enzymes. J Biol Chem. 2016 Sep 16;291(38):19873-87. doi: 10.1074/jbc.M116.739557. Epub, 2016 Jul 29. PMID:27474741 doi:http://dx.doi.org/10.1074/jbc.M116.739557
|
