title: Structure of ALD1, a plant-specific homologue of the universal diaminopimelate aminotransferase enzyme of lysine biosynthesis.
abstract: Diaminopimelate aminotransferase (DAP-AT) is an enzyme in the lysine-biosynthesis pathway. Conversely, ALD1, a close homologue of DAP-AT in plants, uses lysine as a substrate in vitro. Both proteins require pyridoxal-5'-phosphate (PLP) for their activity. The structure of ALD1 from the flowering plant Arabidopsis thaliana (AtALD1) was solved at a resolution of 2.3 Å. Comparison of AtALD1 with the previously solved structure of A. thaliana DAP-AT (AtDAP-AT) revealed similar interactions with PLP despite sequence differences within the PLP-binding site. However, sequence differences between the binding site of AtDAP-AT for malate, a purported mimic of substrate binding, and the corresponding site in AtALD1 led to different interactions. This suggests that either the substrate itself, or the substrate-binding mode, differs in the two proteins, supporting the known in vitro findings.
authors: Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel. vladimir.sobolev@weizmann.ac.il
authors: Vladimir
authors: V
authors: Sobolev
authors: Marvin
authors: M
authors: Edelman
authors: Orly
authors: O
authors: Dym
authors: Tamar
authors: T
authors: Unger
authors: Shira
authors: S
authors: Albeck
authors: Menny
authors: M
authors: Kirma
authors: Gad
authors: G
authors: Galili
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000201:enzymology*; D029681:Arabidopsis Proteins / Q000737:chemistry*; D001665:Binding Sites; D003067:Coenzymes / Q000378:metabolism; D018360:Crystallography, X-Ray; D003960:Diaminopimelic Acid / Q000378:metabolism*; D008239:Lysine / Q000096:biosynthesis*; D008969:Molecular Sequence Data; D011732:Pyridoxal Phosphate / Q000378:metabolism; D016415:Sequence Alignment; D013045:Species Specificity; D040681:Structural Homology, Protein; D013379:Substrate Specificity; D000637:Transaminases / Q000737:chemistry*
chemical_list: D029681:Arabidopsis Proteins; D003067:Coenzymes; D003960:Diaminopimelic Acid; D011732:Pyridoxal Phosphate; C487185:AGD2-LIKE DEFENSE RESPONSE PROTEIN1, Arabidopsis; D000637:Transaminases; D008239:Lysine
keywords: Arabidopsis thaliana; DAP-AT; LPC/CSU analysis; PLP binding
references: Science. 1993 Oct 15;262(5132):380-1
references: 8211158
references: Mol Syst Biol. 2011 Oct 11;7:539
references: 21988835
references: J Mol Biol. 2007 Aug 17;371(3):685-702
references: 17583737
references: Proteins. 2000 May 15;39(3):261-8
references: 10737948
references: J Mol Biol. 2007 Sep 21;372(3):774-97
references: 17681537
references: J Chem Theory Comput. 2011 May 10;7(5):1356-68
references: 26610130
references: J Mol Biol. 2008 Dec 31;384(5):1314-29
references: 18952095
references: Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32
references: 15572765
references: Science. 2003 Aug 29;301(5637):1196-202
references: 12947189
references: Acta Crystallogr D Biol Crystallogr. 2007 Jan;63(Pt 1):32-41
references: 17164524
references: J Mol Biol. 2011 Aug 19;411(3):649-60
references: 21722650
references: Arch Biochem Biophys. 2005 Jan 1;433(1):279-87
references: 15581583
references: J Mol Biol. 2007 Feb 16;366(2):611-25
references: 17174334
references: Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):355-67
references: 21460454
references: Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):72-82
references: 16369096
references: Bioinformatics. 1999 Apr;15(4):327-32
references: 10320401
references: Bioinformatics. 1999 Apr;15(4):305-8
references: 10320398
references: Plant J. 2004 Oct;40(2):200-12
references: 15447647
references: Plant J. 2001 Aug;27(3):203-11
references: 11532166
references: PLoS One. 2011;6(5):e20439
references: 21633707
references: Plant Cell. 2004 Feb;16(2):353-66
references: 14729919
references: Methods Mol Biol. 2008;426:197-208
references: 18542865