2bkw: Difference between revisions

Revision as of 11:22, 22 May 2024

Yeast alanine:glyoxylate aminotransferase YFL030w

Structural highlights

2bkw is a 1 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.57Å
Ligands:	GLV, MSE, PLP
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AGX1_YEAST Has alanine:glyoxylate aminotransferase activity.^[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

We have determined the three-dimensional crystal structure of the protein encoded by the open reading frame YFL030w from Saccharomyces cerevisiae to a resolution of 2.6 A using single wavelength anomalous diffraction. YFL030w is a 385 amino-acid protein with sequence similarity to the aminotransferase family. The structure of the protein reveals a homodimer adopting the fold-type I of pyridoxal 5'-phosphate (PLP)-dependent aminotransferases. The PLP co-factor is covalently bound to the active site in the crystal structure. The protein shows close structural resemblance with the human alanine:glyoxylate aminotransferase (EC 2.6.1.44), an enzyme involved in the hereditary kidney stone disease primary hyperoxaluria type 1. In this paper we show that YFL030w codes for an alanine:glyoxylate aminotransferase, highly specific for its amino donor and acceptor substrates.

Crystal structure and confirmation of the alanine:glyoxylate aminotransferase activity of the YFL030w yeast protein.,Meyer P, Liger D, Leulliot N, Quevillon-Cheruel S, Zhou CZ, Borel F, Ferrer JL, Poupon A, Janin J, van Tilbeurgh H Biochimie. 2005 Dec;87(12):1041-7. Epub 2005 Oct 5. PMID:16226833^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Takada Y, Noguchi T. Characteristics of alanine: glyoxylate aminotransferase from Saccharomyces cerevisiae, a regulatory enzyme in the glyoxylate pathway of glycine and serine biosynthesis from tricarboxylic acid-cycle intermediates. Biochem J. 1985 Oct 1;231(1):157-63. PMID:3933486
↑ Meyer P, Liger D, Leulliot N, Quevillon-Cheruel S, Zhou CZ, Borel F, Ferrer JL, Poupon A, Janin J, van Tilbeurgh H. Crystal structure and confirmation of the alanine:glyoxylate aminotransferase activity of the YFL030w yeast protein. Biochimie. 2005 Dec;87(12):1041-7. Epub 2005 Oct 5. PMID:16226833 doi:10.1016/j.biochi.2005.09.001
↑ Meyer P, Liger D, Leulliot N, Quevillon-Cheruel S, Zhou CZ, Borel F, Ferrer JL, Poupon A, Janin J, van Tilbeurgh H. Crystal structure and confirmation of the alanine:glyoxylate aminotransferase activity of the YFL030w yeast protein. Biochimie. 2005 Dec;87(12):1041-7. Epub 2005 Oct 5. PMID:16226833 doi:10.1016/j.biochi.2005.09.001

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Takada Y, Noguchi T. Characteristics of alanine: glyoxylate aminotransferase from Saccharomyces cerevisiae, a regulatory enzyme in the glyoxylate pathway of glycine and serine biosynthesis from tricarboxylic acid-cycle intermediates. Biochem J. 1985 Oct 1;231(1):157-63. PMID:3933486

[2] Meyer P, Liger D, Leulliot N, Quevillon-Cheruel S, Zhou CZ, Borel F, Ferrer JL, Poupon A, Janin J, van Tilbeurgh H. Crystal structure and confirmation of the alanine:glyoxylate aminotransferase activity of the YFL030w yeast protein. Biochimie. 2005 Dec;87(12):1041-7. Epub 2005 Oct 5. PMID:16226833 doi:10.1016/j.biochi.2005.09.001

[3] Meyer P, Liger D, Leulliot N, Quevillon-Cheruel S, Zhou CZ, Borel F, Ferrer JL, Poupon A, Janin J, van Tilbeurgh H. Crystal structure and confirmation of the alanine:glyoxylate aminotransferase activity of the YFL030w yeast protein. Biochimie. 2005 Dec;87(12):1041-7. Epub 2005 Oct 5. PMID:16226833 doi:10.1016/j.biochi.2005.09.001

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='2bkw' size='340' side='right'caption='[[2bkw]], [[Resolution|resolution]] 2.57&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2bkw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BKW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BKW FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2bkw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BKW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BKW FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLV:GLYOXYLIC+ACID'>GLV</scene>, <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]] 2.57&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLV:GLYOXYLIC+ACID'>GLV</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Alanine--glyoxylate_transaminase Alanine--glyoxylate transaminase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.44 2.6.1.44] </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=2bkw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bkw OCA], [https://pdbe.org/2bkw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bkw RCSB], [https://www.ebi.ac.uk/pdbsum/2bkw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bkw ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/AGX1_YEAST AGX1_YEAST]] Has alanine:glyoxylate aminotransferase activity.<ref>PMID:3933486</ref> <ref>PMID:16226833</ref>
+[https://www.uniprot.org/uniprot/AGX1_YEAST AGX1_YEAST] Has alanine:glyoxylate aminotransferase activity.<ref>PMID:3933486</ref> <ref>PMID:16226833</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 34: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Alanine--glyoxylate transaminase]]
-[[Category: Baker's yeast]]
 [[Category: Large Structures]]
-[[Category: Borel, F]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Ferrer, J L]]
+[[Category: Borel F]]
-[[Category: Janin, J]]
+[[Category: Ferrer JL]]
-[[Category: Leulliot, N]]
+[[Category: Janin J]]
-[[Category: Liger, D]]
+[[Category: Leulliot N]]
-[[Category: Meyer, P]]
+[[Category: Liger D]]
-[[Category: Poupon, A]]
+[[Category: Meyer P]]
-[[Category: Quevillon-Cheruel, S]]
+[[Category: Poupon A]]
-[[Category: Tilbeurgh, H van]]
+[[Category: Quevillon-Cheruel S]]
-[[Category: Zhou, C Z]]
+[[Category: Zhou CZ]]
-[[Category: Analine-glyoxylate aminotransferase]]
+[[Category: Van Tilbeurgh H]]
-[[Category: Glycolate pathway]]
-[[Category: Pyridoxal-5-phosphate]]
-[[Category: Sad]]
-[[Category: Transferase]]

2bkw: Difference between revisions

Revision as of 11:22, 22 May 2024

Yeast alanine:glyoxylate aminotransferase YFL030w

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

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