|
|
| Line 3: |
Line 3: |
| | <StructureSection load='2dab' size='340' side='right'caption='[[2dab]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='2dab' size='340' side='right'caption='[[2dab]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2dab]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacym Bacym]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DAB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DAB FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2dab]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._YM-1 Bacillus sp. YM-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DAB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DAB 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]] 2Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/D-amino-acid_transaminase D-amino-acid transaminase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.21 2.6.1.21] </span></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dab OCA], [https://pdbe.org/2dab PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dab RCSB], [https://www.ebi.ac.uk/pdbsum/2dab PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dab 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=2dab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dab OCA], [https://pdbe.org/2dab PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dab RCSB], [https://www.ebi.ac.uk/pdbsum/2dab PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dab ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/DAAA_BACYM DAAA_BACYM]] Acts on the D-isomers of alanine, leucine, aspartate, glutamate, aminobutyrate, norvaline and asparagine. The enzyme transfers an amino group from a substrate D-amino acid to the pyridoxal phosphate cofactor to form pyridoxamine and an alpha-keto acid in the first half-reaction. The second-half reaction is the reverse of the first, transferring the amino group from the pyridoxamine to a second alpha-keto acid to form the product D-amino acid via a ping-pong mechanism. This is an important process in the formation of D-alanine and D-glutamate, which are essential bacterial cell wall components.<ref>PMID:2914916</ref> <ref>PMID:9538014</ref>
| + | [https://www.uniprot.org/uniprot/DAAA_BACYM DAAA_BACYM] Acts on the D-isomers of alanine, leucine, aspartate, glutamate, aminobutyrate, norvaline and asparagine. The enzyme transfers an amino group from a substrate D-amino acid to the pyridoxal phosphate cofactor to form pyridoxamine and an alpha-keto acid in the first half-reaction. The second-half reaction is the reverse of the first, transferring the amino group from the pyridoxamine to a second alpha-keto acid to form the product D-amino acid via a ping-pong mechanism. This is an important process in the formation of D-alanine and D-glutamate, which are essential bacterial cell wall components.<ref>PMID:2914916</ref> <ref>PMID:9538014</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 37: |
Line 37: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacym]] | + | [[Category: Bacillus sp. YM-1]] |
| - | [[Category: D-amino-acid transaminase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Esaki, N]] | + | [[Category: Esaki N]] |
| - | [[Category: Kashima, A]] | + | [[Category: Kashima A]] |
| - | [[Category: Kishimoto, K]] | + | [[Category: Kishimoto K]] |
| - | [[Category: Peisach, D]] | + | [[Category: Peisach D]] |
| - | [[Category: Petsko, G A]] | + | [[Category: Petsko GA]] |
| - | [[Category: Ringe, D]] | + | [[Category: Ringe D]] |
| - | [[Category: Sugio, S]] | + | [[Category: Sugio S]] |
| - | [[Category: Yoshimura, T]] | + | [[Category: Yoshimura T]] |
| - | [[Category: Alpha-ketoglutamic acid]]
| + | |
| - | [[Category: Aminotransferase]]
| + | |
| - | [[Category: D-alanine]]
| + | |
| - | [[Category: D-amino acid]]
| + | |
| - | [[Category: Pyridoxal-5'-phosphate]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
DAAA_BACYM Acts on the D-isomers of alanine, leucine, aspartate, glutamate, aminobutyrate, norvaline and asparagine. The enzyme transfers an amino group from a substrate D-amino acid to the pyridoxal phosphate cofactor to form pyridoxamine and an alpha-keto acid in the first half-reaction. The second-half reaction is the reverse of the first, transferring the amino group from the pyridoxamine to a second alpha-keto acid to form the product D-amino acid via a ping-pong mechanism. This is an important process in the formation of D-alanine and D-glutamate, which are essential bacterial cell wall components.[1] [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 PubMed
The leucine-to-alanine mutation at residue 201 of D-amino acid aminotransferase provides a unique enzyme which gradually loses its activity while catalyzing the normal transamination; the co-enzyme form is converted from pyridoxal 5'-phosphate to pyridoxamine 5'-phosphate upon the inactivation [Kishimoto,K., Yoshimura,T., Esaki,N., Sugio,S., Manning,J.M. and Soda,K. (1995) J. Biochem., 117, 691-696]. Crystal structures of both co-enzyme forms of the mutant enzyme have been determined at 2.0 A resolution: they are virtually identical, and are quite similar to that of the wild-type enzyme. Significant differences in both forms of the mutant are localized only on the bound co-enzyme, the side chains of Lys145 and Tyr31, and a water molecule sitting on the putative substrate binding site. Detailed comparisons of the structures of the mutant, together with that of the pyridoxamine-5'-phosphate form of the wild-type enzyme, imply that Leu201 would play a crucial role in the transamination reaction by keeping the pyridoxyl ring in the proper location without disturbing its oscillating motion, although the residue seems to not be especially important for the structural integrity of the enzyme.
Crystal structures of L201A mutant of D-amino acid aminotransferase at 2.0 A resolution: implication of the structural role of Leu201 in transamination.,Sugio S, Kashima A, Kishimoto K, Peisach D, Petsko GA, Ringe D, Yoshimura T, Esaki N Protein Eng. 1998 Aug;11(8):613-9. PMID:9749913[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Tanizawa K, Masu Y, Asano S, Tanaka H, Soda K. Thermostable D-amino acid aminotransferase from a thermophilic Bacillus species. Purification, characterization, and active site sequence determination. J Biol Chem. 1989 Feb 15;264(5):2445-9. PMID:2914916
- ↑ Peisach D, Chipman DM, Van Ophem PW, Manning JM, Ringe D. Crystallographic study of steps along the reaction pathway of D-amino acid aminotransferase. Biochemistry. 1998 Apr 7;37(14):4958-67. PMID:9538014 doi:10.1021/bi972884d
- ↑ Sugio S, Kashima A, Kishimoto K, Peisach D, Petsko GA, Ringe D, Yoshimura T, Esaki N. Crystal structures of L201A mutant of D-amino acid aminotransferase at 2.0 A resolution: implication of the structural role of Leu201 in transamination. Protein Eng. 1998 Aug;11(8):613-9. PMID:9749913
|
