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| | <StructureSection load='1u08' size='340' side='right'caption='[[1u08]], [[Resolution|resolution]] 2.35Å' scene=''> | | <StructureSection load='1u08' size='340' side='right'caption='[[1u08]], [[Resolution|resolution]] 2.35Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1u08]] is a 2 chain structure with sequence from [http://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=1U08 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1U08 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1u08]] is a 2 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=1U08 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U08 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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]] 2.35Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dju|1dju]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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">ybdL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1u08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u08 OCA], [https://pdbe.org/1u08 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u08 RCSB], [https://www.ebi.ac.uk/pdbsum/1u08 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u08 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1u08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u08 OCA], [http://pdbe.org/1u08 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u08 RCSB], [http://www.ebi.ac.uk/pdbsum/1u08 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1u08 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/YBDL_ECOLI YBDL_ECOLI]] Shows aminotransferase activity with methionine and histidine as substrates, and to a lesser extent also with phenylalanine. | + | [https://www.uniprot.org/uniprot/YBDL_ECOLI YBDL_ECOLI] Shows aminotransferase activity with methionine and histidine as substrates, and to a lesser extent also with phenylalanine. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Cambillau, C]] | + | [[Category: Cambillau C]] |
| - | [[Category: Campanacci, V]] | + | [[Category: Campanacci V]] |
| - | [[Category: Dolzan, M]] | + | [[Category: Dolzan M]] |
| - | [[Category: Johansson, K]] | + | [[Category: Johansson K]] |
| - | [[Category: Roig-Zamboni, V]] | + | [[Category: Roig-Zamboni V]] |
| - | [[Category: Schneider, G]] | + | [[Category: Schneider G]] |
| - | [[Category: Tegoni, M]] | + | [[Category: Tegoni M]] |
| - | [[Category: Alpha beta protein]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
YBDL_ECOLI Shows aminotransferase activity with methionine and histidine as substrates, and to a lesser extent also with phenylalanine.
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 PubMed
The ybdL gene of Escherichia coli codes for a protein of unknown function. Sequence analysis showed moderate homology to several vitamin B(6) dependent enzymes, suggesting that it may bind pyridoxal-5'-phosphate. The structure analysis of YbdL to 2.35 A resolution by protein crystallography verifies that it is a PLP dependent enzyme of fold type I, the typical aspartate aminotransferase fold. The active site contains a bound pyridoxal-5'-phosphate, covalently attached to the conserved active site lysine residue Lys236. The pattern of conserved amino acids in the putative substrate binding pocket of the enzyme reveals that it is most closely related to a hyperthermophilic aromatic residue aminotransferase from the archeon Pyrococcus horikoshii. Activity tests with 10 amino acids as amino-donors reveal, however, a preference for Met, followed by His and Phe, results which can be rationalized by modelization studies.
Crystal structure and reactivity of YbdL from Escherichia coli identify a methionine aminotransferase function.,Dolzan M, Johansson K, Roig-Zamboni V, Campanacci V, Tegoni M, Schneider G, Cambillau C FEBS Lett. 2004 Jul 30;571(1-3):141-6. PMID:15280032[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Dolzan M, Johansson K, Roig-Zamboni V, Campanacci V, Tegoni M, Schneider G, Cambillau C. Crystal structure and reactivity of YbdL from Escherichia coli identify a methionine aminotransferase function. FEBS Lett. 2004 Jul 30;571(1-3):141-6. PMID:15280032 doi:10.1016/j.febslet.2004.06.075
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