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| - | [[Image:4daa.gif|left|200px]] | + | ==CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE IN PYRIDOXAL-5'-PHOSPHATE (PLP) FORM== |
| | + | <StructureSection load='4daa' size='340' side='right' caption='[[4daa]], [[Resolution|resolution]] 2.40Å' scene=''> |
| | + | == Structural highlights == |
| | + | <table><tr><td colspan='2'>[[4daa]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacym Bacym]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DAA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DAA FirstGlance]. <br> |
| | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| | + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-amino-acid_transaminase D-amino-acid transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.21 2.6.1.21] </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=4daa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4daa OCA], [http://pdbe.org/4daa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4daa RCSB], [http://www.ebi.ac.uk/pdbsum/4daa PDBsum]</span></td></tr> |
| | + | </table> |
| | + | == Function == |
| | + | [[http://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 == |
| | + | [[Image:Consurf_key_small.gif|200px|right]] |
| | + | Check<jmol> |
| | + | <jmolCheckbox> |
| | + | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/da/4daa_consurf.spt"</scriptWhenChecked> |
| | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | + | <text>to colour the structure by Evolutionary Conservation</text> |
| | + | </jmolCheckbox> |
| | + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=4daa ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | The three-dimensional structures of two forms of the D-amino acid aminotransferase (D-aAT) from Bacillus sp. YM-1 have been determined crystallographically: the pyridoxal phosphate (PLP) form and a complex with the reduced analogue of the external aldimine, N-(5'-phosphopyridoxyl)-d-alanine (PPDA). Together with the previously reported pyridoxamine phosphate form of the enzyme [Sugio et al. (1995) Biochemistry 34, 9661], these structures allow us to describe the pathway of the enzymatic reaction in structural terms. A major determinant of the enzyme's stereospecificity for D-amino acids is a group of three residues (Tyr30, Arg98, and His100, with the latter two contributed by the neighboring subunit) forming four hydrogen bonds to the substrate alpha-carboxyl group. The replacement by hydrophobic groups of the homologous residues of the branched chain L-amino acid aminotransferase (which has a similar fold) could explain its opposite stereospecificity. As in L-aspartate aminotransferase (L-AspAT), the cofactor in D-aAT tilts (around its phosphate group and N1 as pivots) away from the catalytic lysine 145 and the protein face in the course of the reaction. Unlike L-AspAT, D-aAT shows no other significant conformational changes during the reaction. |
| | | | |
| - | {{Structure
| + | Crystallographic study of steps along the reaction pathway of D-amino acid aminotransferase.,Peisach D, Chipman DM, Van Ophem PW, Manning JM, Ringe D Biochemistry. 1998 Apr 7;37(14):4958-67. PMID:9538014<ref>PMID:9538014</ref> |
| - | |PDB= 4daa |SIZE=350|CAPTION= <scene name='initialview01'>4daa</scene>, resolution 2.4Å
| + | |
| - | |SITE= <scene name='pdbsite=ASA:Active+Site+A'>ASA</scene> and <scene name='pdbsite=ASB:Essentially+The+Same+As+Asa'>ASB</scene>
| + | |
| - | |LIGAND= <scene name='pdbligand=PLP:PYRIDOXAL-5'-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
| + | |
| - | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/D-amino-acid_transaminase D-amino-acid transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.21 2.6.1.21] </span>
| + | |
| - | |GENE=
| + | |
| - | |DOMAIN=
| + | |
| - | |RELATEDENTRY=
| + | |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4daa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4daa OCA], [http://www.ebi.ac.uk/pdbsum/4daa PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=4daa RCSB]</span>
| + | |
| - | }}
| + | |
| | | | |
| - | '''CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE IN PYRIDOXAL-5'-PHOSPHATE (PLP) FORM'''
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | + | </div> |
| | + | <div class="pdbe-citations 4daa" style="background-color:#fffaf0;"></div> |
| | | | |
| - | | + | ==See Also== |
| - | ==Overview== | + | *[[Aminotransferase|Aminotransferase]] |
| - | The three-dimensional structures of two forms of the D-amino acid aminotransferase (D-aAT) from Bacillus sp. YM-1 have been determined crystallographically: the pyridoxal phosphate (PLP) form and a complex with the reduced analogue of the external aldimine, N-(5'-phosphopyridoxyl)-d-alanine (PPDA). Together with the previously reported pyridoxamine phosphate form of the enzyme [Sugio et al. (1995) Biochemistry 34, 9661], these structures allow us to describe the pathway of the enzymatic reaction in structural terms. A major determinant of the enzyme's stereospecificity for D-amino acids is a group of three residues (Tyr30, Arg98, and His100, with the latter two contributed by the neighboring subunit) forming four hydrogen bonds to the substrate alpha-carboxyl group. The replacement by hydrophobic groups of the homologous residues of the branched chain L-amino acid aminotransferase (which has a similar fold) could explain its opposite stereospecificity. As in L-aspartate aminotransferase (L-AspAT), the cofactor in D-aAT tilts (around its phosphate group and N1 as pivots) away from the catalytic lysine 145 and the protein face in the course of the reaction. Unlike L-AspAT, D-aAT shows no other significant conformational changes during the reaction.
| + | == References == |
| - | | + | <references/> |
| - | ==About this Structure== | + | __TOC__ |
| - | 4DAA is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DAA OCA].
| + | </StructureSection> |
| - | | + | [[Category: Bacym]] |
| - | ==Reference==
| + | |
| - | Crystallographic study of steps along the reaction pathway of D-amino acid aminotransferase., Peisach D, Chipman DM, Van Ophem PW, Manning JM, Ringe D, Biochemistry. 1998 Apr 7;37(14):4958-67. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9538014 9538014]
| + | |
| - | [[Category: Bacillus sp.]] | + | |
| | [[Category: D-amino-acid transaminase]] | | [[Category: D-amino-acid transaminase]] |
| - | [[Category: Single protein]]
| + | [[Category: Chipman, D M]] |
| - | [[Category: Chipman, D M.]] | + | [[Category: Peisach, D]] |
| - | [[Category: Peisach, D.]] | + | [[Category: Ringe, D]] |
| - | [[Category: Ringe, D.]] | + | [[Category: Aminotransferase]] |
| - | [[Category: aminotransferase]] | + | [[Category: Pyridoxal phosphate]] |
| - | [[Category: pyridoxal phosphate]] | + | [[Category: Transaminase]] |
| - | [[Category: transaminase]] | + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:38:28 2008''
| + | |
| 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 three-dimensional structures of two forms of the D-amino acid aminotransferase (D-aAT) from Bacillus sp. YM-1 have been determined crystallographically: the pyridoxal phosphate (PLP) form and a complex with the reduced analogue of the external aldimine, N-(5'-phosphopyridoxyl)-d-alanine (PPDA). Together with the previously reported pyridoxamine phosphate form of the enzyme [Sugio et al. (1995) Biochemistry 34, 9661], these structures allow us to describe the pathway of the enzymatic reaction in structural terms. A major determinant of the enzyme's stereospecificity for D-amino acids is a group of three residues (Tyr30, Arg98, and His100, with the latter two contributed by the neighboring subunit) forming four hydrogen bonds to the substrate alpha-carboxyl group. The replacement by hydrophobic groups of the homologous residues of the branched chain L-amino acid aminotransferase (which has a similar fold) could explain its opposite stereospecificity. As in L-aspartate aminotransferase (L-AspAT), the cofactor in D-aAT tilts (around its phosphate group and N1 as pivots) away from the catalytic lysine 145 and the protein face in the course of the reaction. Unlike L-AspAT, D-aAT shows no other significant conformational changes during the reaction.
Crystallographic study of steps along the reaction pathway of D-amino acid aminotransferase.,Peisach D, Chipman DM, Van Ophem PW, Manning JM, Ringe D Biochemistry. 1998 Apr 7;37(14):4958-67. PMID:9538014[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
- ↑ 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
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