5daa: Difference between revisions

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-[[Image:5daa.png|left|200px]]
-{{STRUCTURE_5daa|  PDB=5daa  |  SCENE=  }}
+==E177K MUTANT OF D-AMINO ACID AMINOTRANSFERASE COMPLEXED WITH PYRIDOXAMINE-5'-PHOSPHATE==
+<StructureSection load='5daa' size='340' side='right'caption='[[5daa]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5daa]] 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=5DAA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DAA FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</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=5daa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5daa OCA], [https://pdbe.org/5daa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5daa RCSB], [https://www.ebi.ac.uk/pdbsum/5daa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5daa ProSAT]</span></td></tr>
+</table>
+== 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/5daa_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=5daa ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+D-Amino acid transaminase is a bacterial enzyme that uses pyridoxal phosphate (PLP) as a cofactor to catalyze the conversion of D-amino acids into their corresponding alpha-keto acids. This enzyme has already been established as a target for novel antibacterial agents through suicide inactivation by a number of compounds. To improve their potency and specificity, the detailed enzyme mechanism, especially the role of its PLP cofactor, is under investigation. Many PLP-dependent transaminases have a negatively charged amino acid residue forming a salt-bridge with the pyridine nitrogen of its cofactor that promotes its protonation to stabilize the formation of a ketimine intermediate, which is subsequently hydrolyzed in the normal transaminase reaction pathway. However, alanine racemase has a positively charged arginine held rigidly in place by an extensive hydrogen bond network that may destabilize the ketimine intermediate, and make it too short-lived for a transaminase type of hydrolysis to occur. To test this hypothesis, we changed Glu-177 into a titratable, positively charged lysine (E177K). The crystal structure of this mutant shows that the positive charge of the newly introduced lysine side chain points away from the nitrogen of the cofactor, which may be due to electrostatic repulsions not being overcome by a hydrogen bond network such as found in alanine racemase. This mutation makes the active site more accessible, as exemplified by both biochemical and crystallographic data: CD measurements indicated a change in the microenvironment of the protein, some SH groups become more easily titratable, and at pH 9.0 the PMP peak appeared around 315 nm rather than at 330 nm. The ability of this mutant to convert L-alanine into D-alanine increased about 10-fold compared to wild-type and to about the same extent as found with other active site mutants. On the other hand, the specific activity of the E177K mutant decreased more than 1000-fold compared to wild-type. Furthermore, titration with L-alanine resulted in the appearance of an enzyme-substrate quinonoid intermediate absorbing around 500 nm, which is not observed with usual substrates or with the wild-type enzyme in the presence of L-alanine. The results overall indicate the importance of charged amino acid side chains relative to the coenzyme to maintain high catalytic efficiency.
-===E177K MUTANT OF D-AMINO ACID AMINOTRANSFERASE COMPLEXED WITH PYRIDOXAMINE-5'-PHOSPHATE===
+Effects of the E177K mutation in D-amino acid transaminase. Studies on an essential coenzyme anchoring group that contributes to stereochemical fidelity.,van Ophem PW, Peisach D, Erickson SD, Soda K, Ringe D, Manning JM Biochemistry. 1999 Jan 26;38(4):1323-31. PMID:9930994<ref>PMID:9930994</ref>
-{{ABSTRACT_PUBMED_9930994}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 5daa" style="background-color:#fffaf0;"></div>
-[[5daa]] is a 2 chain structure of [[Aspartate Aminotransferase]] with 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=5DAA OCA].
 ==See Also==
-*[[Aspartate Aminotransferase|Aspartate Aminotransferase]]
+*[[Aminotransferase 3D structures|Aminotransferase 3D structures]]
+*[[Aspartate aminotransferase 3D structures|Aspartate aminotransferase 3D structures]]
-==Reference==
+== References ==
-<ref group="xtra">PMID:009930994</ref><references group="xtra"/>
+<references/>
-[[Category: Bacillus sp.]]
+__TOC__
-[[Category: D-amino-acid transaminase]]
+</StructureSection>
-[[Category: Peisach, D.]]
+[[Category: Bacillus sp. YM-1]]
-[[Category: Ringe, D.]]
+[[Category: Large Structures]]
-[[Category: Aminotransferase]]
+[[Category: Peisach D]]
-[[Category: Pyridoxal phosphate]]
+[[Category: Ringe D]]
-[[Category: Transaminase]]
-[[Category: Transferase]]