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[[Image:1daa.gif|left|200px]]


{{Structure
==CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE COMPLEXED WITH PYRIDOXAL-5'-PHOSPHATE==
|PDB= 1daa |SIZE=350|CAPTION= <scene name='initialview01'>1daa</scene>, resolution 1.94&Aring;
<StructureSection load='1daa' size='340' side='right'caption='[[1daa]], [[Resolution|resolution]] 1.94&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=PLP:PYRIDOXAL-5&#39;-PHOSPHATE'>PLP</scene>
<table><tr><td colspan='2'>[[1daa]] 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=1DAA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DAA FirstGlance]. <br>
|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>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.94&#8491;</td></tr>
|GENE=  
<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>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1daa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1daa OCA], [https://pdbe.org/1daa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1daa RCSB], [https://www.ebi.ac.uk/pdbsum/1daa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1daa ProSAT]</span></td></tr>
|RELATEDENTRY=
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1daa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1daa OCA], [http://www.ebi.ac.uk/pdbsum/1daa PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1daa RCSB]</span>
== 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>
== 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/1daa_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=1daa ConSurf].
<div style="clear:both"></div>


'''CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE COMPLEXED WITH PYRIDOXAL-5'-PHOSPHATE'''
==See Also==
 
*[[Aminotransferase 3D structures|Aminotransferase 3D structures]]
 
*[[Aspartate aminotransferase 3D structures|Aspartate aminotransferase 3D structures]]
==Overview==
== References ==
The three-dimensional structure of D-amino acid aminotransferase (D-AAT) in the pyridoxamine phosphate form has been determined crystallographically. The fold of this pyridoxal phosphate (PLP)-containing enzyme is completely different from those of any of the other enzymes that utilize PLP as part of their mechanism and whose structures are known. However, there are some striking similarities between the active sites of D-AAT and the corresponding enzyme that transaminates L-amino acids, L-aspartate aminotransferase. These similarities represent convergent evolution to a common solution of the problem of enforcing transamination chemistry on the PLP cofactor. Implications of these similarities are discussed in terms of their possible roles in the stabilization of intermediates of a transamination reaction. In addition, sequence similarity between D-AAT and branched chain L-amino acid aminotransferase suggests that this latter enzyme will also have a fold similar to that of D-AAT.
<references/>
 
__TOC__
==About this Structure==
</StructureSection>
1DAA 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=1DAA OCA].
[[Category: Bacillus sp. YM-1]]
 
[[Category: Large Structures]]
==Reference==
[[Category: Peisach D]]
Crystal structure of a D-amino acid aminotransferase: how the protein controls stereoselectivity., Sugio S, Petsko GA, Manning JM, Soda K, Ringe D, Biochemistry. 1995 Aug 1;34(30):9661-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7626635 7626635]
[[Category: Ringe D]]
[[Category: Bacillus sp.]]
[[Category: Sugio S]]
[[Category: D-amino-acid transaminase]]
[[Category: Single protein]]
[[Category: Peisach, D.]]
[[Category: Ringe, D.]]
[[Category: Sugio, S.]]
[[Category: aminotransferase]]
[[Category: d-alanine]]
[[Category: d-amino acid]]
[[Category: pyridoxal phosphate]]
[[Category: transferase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:37:42 2008''

Latest revision as of 09:51, 7 February 2024

CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE COMPLEXED WITH PYRIDOXAL-5'-PHOSPHATECRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE COMPLEXED WITH PYRIDOXAL-5'-PHOSPHATE

Structural highlights

1daa is a 2 chain structure with sequence from Bacillus sp. YM-1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.94Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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.

See Also

References

  1. ↑ 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
  2. ↑ 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

1daa, resolution 1.94Å

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