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| | ==Crystal structure of benzaldehyde lyase in complex with the inhibitor MBP== | | ==Crystal structure of benzaldehyde lyase in complex with the inhibitor MBP== |
| - | <StructureSection load='3d7k' size='340' side='right' caption='[[3d7k]], [[Resolution|resolution]] 2.49Å' scene=''> | + | <StructureSection load='3d7k' size='340' side='right'caption='[[3d7k]], [[Resolution|resolution]] 2.49Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3d7k]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D7K FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3d7k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D7K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D7K FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=D7K:3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(S)-HYDROXY[(R)-HYDROXY(METHOXY)PHOSPHORYL]PHENYLMETHYL}-5-(2-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM'>D7K</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]] 2.49Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bznB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 Pseudomonas fluorescens])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=D7K:3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(S)-HYDROXY[(R)-HYDROXY(METHOXY)PHOSPHORYL]PHENYLMETHYL}-5-(2-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM'>D7K</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Benzoin_aldolase Benzoin aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.38 4.1.2.38] </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=3d7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d7k OCA], [https://pdbe.org/3d7k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d7k RCSB], [https://www.ebi.ac.uk/pdbsum/3d7k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d7k ProSAT]</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=3d7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d7k OCA], [http://pdbe.org/3d7k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3d7k RCSB], [http://www.ebi.ac.uk/pdbsum/3d7k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3d7k ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q9F4L3_PSEFL Q9F4L3_PSEFL] |
| | == 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: Benzoin aldolase]] | + | [[Category: Large Structures]] |
| | [[Category: Pseudomonas fluorescens]] | | [[Category: Pseudomonas fluorescens]] |
| - | [[Category: Brandt, G S]] | + | [[Category: Brandt GS]] |
| - | [[Category: Bal with cofactor-inhibitor adduct]]
| + | |
| - | [[Category: Flavoprotein]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Thiamine pyrophosphate]]
| + | |
| Structural highlights
Function
Q9F4L3_PSEFL
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
Benzaldehyde lyase (BAL) catalyzes the reversible cleavage of ( R)-benzoin to benzaldehyde utilizing thiamin diphosphate and Mg (2+) as cofactors. The enzyme is important for the chemoenzymatic synthesis of a wide range of compounds via its carboligation reaction mechanism. In addition to its principal functions, BAL can slowly decarboxylate aromatic amino acids such as benzoylformic acid. It is also intriguing mechanistically due to the paucity of acid-base residues at the active center that can participate in proton transfer steps thought to be necessary for these types of reactions. Here methyl benzoylphosphonate, an excellent electrostatic analogue of benzoylformic acid, is used to probe the mechanism of benzaldehyde lyase. The structure of benzaldehyde lyase in its covalent complex with methyl benzoylphosphonate was determined to 2.49 A (Protein Data Bank entry 3D7K ) and represents the first structure of this enzyme with a compound bound in the active site. No large structural reorganization was detected compared to the complex of the enzyme with thiamin diphosphate. The configuration of the predecarboxylation thiamin-bound intermediate was clarified by the structure. Both spectroscopic and X-ray structural studies are consistent with inhibition resulting from the binding of MBP to the thiamin diphosphate in the active centers. We also delineated the role of His29 (the sole potential acid-base catalyst in the active site other than the highly conserved Glu50) and Trp163 in cofactor activation and catalysis by benzaldehyde lyase.
Probing the Active Center of Benzaldehyde Lyase with Substitutions and the Pseudosubstrate Analogue Benzoylphosphonic Acid Methyl Ester.,Brandt GS, Nemeria N, Chakraborty S, McLeish MJ, Yep A, Kenyon GL, Petsko GA, Jordan F, Ringe D Biochemistry. 2008 Jun 21;. PMID:18570438[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Brandt GS, Nemeria N, Chakraborty S, McLeish MJ, Yep A, Kenyon GL, Petsko GA, Jordan F, Ringe D. Probing the Active Center of Benzaldehyde Lyase with Substitutions and the Pseudosubstrate Analogue Benzoylphosphonic Acid Methyl Ester. Biochemistry. 2008 Jun 21;. PMID:18570438 doi:10.1021/bi8004413
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