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CATH domain | Related DB codes (homologues) |
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3.20.10.10 : D-amino Acid Aminotransferase; Chain A, domain 2 | D00106 | 3.30.470.10 : D-amino Acid Aminotransferase; Chain A, domain 1 | D00106 |
Enzyme Name | UniProtKB | KEGG |
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| P19938 |
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Protein name | D-alanine aminotransferase | D-amino-acid transaminaseD-aspartate transaminaseD-alanine aminotransferaseD-aspartic aminotransferaseD-alanine-D-glutamate transaminaseD-alanine transaminaseD-amino acid aminotransferase |
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Synonyms | EC 2.6.1.21D-amino acid aminotransferaseD-amino acid transaminaseDAATD-aspartate aminotransferase |
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Pfam | PF01063 (Aminotran_4) [Graphical view]
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UniProtKB:Accession Number | P19938 |
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Entry name | DAAA_BACYM |
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Activity | D-alanine + 2-oxoglutarate = pyruvate + D- glutamate. |
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Subunit | Homodimer. |
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Subcellular location |
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Cofactor | Pyridoxal phosphate. |
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Compound table: links to PDB-related databases & PoSSuM |
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| Cofactors | Substrates | Products | intermediates |
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KEGG-id | C00018 | C00133 | C00026 | C00022 | C00217 | I00029 | I00032 | I00030 |
| C00647 | I00006 | I00033 | I00031 |
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Compound | Pyridoxal phosphate | D-Alanine | 2-Oxoglutarate | Pyruvate | D-Glutamate | External aldimine intermediate (initial stage:PLP-D-Ala) | Quinonoid Intermediate-1 (PLP-Ala) | Ketimine intermediate-1 (PLP-Ala) | Tetrahedral intermediate from ketimine to PMP | Pyridoxamine phosphate (PMP) | Ketimine intermediate-2 (PLP-Glu) | Quinonoid Intermediate-2 (PLP-Glu) | External aldimine intermediate (final stage:PLP-D-Glu) |
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Type | aromatic ring (with nitrogen atoms),phosphate group/phosphate ion | amino acids | carbohydrate,carboxyl group | carbohydrate,carboxyl group | amino acids,carboxyl group |
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ChEBI | 18405
| 15570 57416
| 30915
| 32816
| 15966
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PubChem | 1051
| 71080 7311725
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| 23327
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1a0gA01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | | | Unbound | | | |
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1a0gB01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | | | Unbound | | | |
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1daaA01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | | | Unbound | | | |
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1daaB01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | | | Unbound | | | |
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1g2wA01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Analogue:ACT | Unbound | Unbound | Unbound | | | Unbound | | | |
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1g2wB01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Analogue:ACT | Unbound | Unbound | Unbound | | | Unbound | | | |
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2daaA01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | | | Unbound | | | |
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2daaB01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | | | Unbound | | | |
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2dabA01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | | | Unbound | | | |
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2dabB01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | | | Unbound | | | |
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3daaA01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | | | Unbound | | | |
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3daaB01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | | | Unbound | | | |
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4daaA01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | | | Unbound | | | |
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4daaB01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | | | Unbound | | | |
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5daaA01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | | | Unbound | | | |
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5daaB01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | | | Unbound | | | |
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1a0gA02 |  |  |  |  |  |  |  | Analogue:PMP | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | | | Intermediate-bound:PMP | | | |
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1a0gB02 |  |  |  |  |  |  |  | Analogue:PMP | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | | | Intermediate-bound:PMP | | | |
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1daaA02 |  |  |  |  |  |  |  | Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | | | Unbound | | | |
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1daaB02 |  |  |  |  |  |  |  | Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | | | Unbound | | | |
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1g2wA02 |  |  |  |  |  |  |  | Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | | | Unbound | | | |
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1g2wB02 |  |  |  |  |  |  |  | Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | | | Unbound | | | |
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2daaA02 |  |  |  |  |  |  |  | Analogue:DCS | Unbound | Unbound | Unbound | Unbound | Unbound | Intermediate-analogue:DCS | | | Unbound | | | |
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2daaB02 |  |  |  |  |  |  |  | Analogue:DCS | Unbound | Unbound | Unbound | Unbound | Unbound | Intermediate-analogue:DCS | | | Unbound | | | |
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2dabA02 |  |  |  |  |  |  |  | Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | | | Unbound | | | |
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2dabB02 |  |  |  |  |  |  |  | Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | | | Unbound | | | |
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3daaA02 |  |  |  |  |  |  |  | Analogue:PDD | Unbound | Unbound | Unbound | Unbound | Intermediate-bound:PDD | Unbound | | | Unbound | | | |
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3daaB02 |  |  |  |  |  |  |  | Analogue:PDD | Unbound | Unbound | Unbound | Unbound | Intermediate-bound:PDD | Unbound | | | Unbound | | | |
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4daaA02 |  |  |  |  |  |  |  | Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | | | Unbound | | | |
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4daaB02 |  |  |  |  |  |  |  | Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | | | Unbound | | | |
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5daaA02 |  |  |  |  |  |  |  | Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | | | Unbound | | | |
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5daaB02 |  |  |  |  |  |  |  | Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | | | Unbound | | | |
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References for Catalytic Mechanism | References | Sections | No. of steps in catalysis |
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[8] | Scheme I |
| [9] | Fig.1, p.9661-9662, p.9666-9667 |
| [13] | Fig.1, Fig.2, p.181-182 |
| [14] | Fig.1 |
| [16] | Fig.1, Fig.8, p.4964 |
| [17] | Fig.1, p.765 |
| [19] | Fig.1, p.617-618 |
| [20] | Fig.1, Fig.3, p.696-697, p.698-699 |
| [21] | p.1330-1331 |
| [22] | Fig.3, Fig.10, p.143-149, p.155-156 |
| [25] | Fig.2, p.R5 |
| [26] | Fig.1, Fig.2, Fig.3, p.375-378 |
| [27] | Fig.1 |
| [28] | Fig.1 |
|
references | [1] |
---|
PubMed ID | 4950474 |
---|
Journal | Adv Enzymol Relat Areas Mol Biol |
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Year | 1971 |
---|
Volume | 35 |
---|
Pages | 79-134 |
---|
Authors | Dunathan HC |
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Title | Stereochemical aspects of pyridoxal phosphate catalysis. |
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[2] |
---|
PubMed ID | 2713327 |
---|
Journal | Biochemistry |
---|
Year | 1989 |
---|
Volume | 28 |
---|
Pages | 510-6 |
---|
Authors | Martinez del Pozo A, Merola M, Ueno H, Manning JM, Tanizawa K, Nishimura K, Asano S, Tanaka H, Soda K, Ringe D, et al |
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Title | Activity and spectroscopic properties of bacterial D-amino acid transaminase after multiple site-directed mutagenesis of a single tryptophan residue. |
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[3] |
---|
PubMed ID | 2496746 |
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Journal | Biochemistry |
---|
Year | 1989 |
---|
Volume | 28 |
---|
Pages | 505-9 |
---|
Authors | Merola M, Martinez del Pozo A, Ueno H, Recsei P, Di Donato A, Manning JM, Tanizawa K, Masu Y, Asano S, Tanaka H, et al |
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Title | Site-directed mutagenesis of the cysteinyl residues and the active-site serine residue of bacterial D-amino acid transaminase. |
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[4] |
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PubMed ID | 2914916 |
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Journal | J Biol Chem |
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Year | 1989 |
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Volume | 264 |
---|
Pages | 2445-9 |
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Authors | Tanizawa K, Masu Y, Asano S, Tanaka H, Soda K |
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Title | Thermostable D-amino acid aminotransferase from a thermophilic Bacillus species. Purification, characterization, and active site sequence determination. |
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[5] |
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PubMed ID | 2125047 |
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Journal | J Biol Chem |
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Year | 1990 |
---|
Volume | 265 |
---|
Pages | 22306-12 |
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Authors | Futaki S, Ueno H, Martinez del Pozo A, Pospischil MA, Manning JM, Ringe D, Stoddard B, Tanizawa K, Yoshimura T, Soda K |
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Title | Substitution of glutamine for lysine at the pyridoxal phosphate binding site of bacterial D-amino acid transaminase. Effects of exogenous amines on the slow formation of intermediates. |
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[6] |
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PubMed ID | 1902115 |
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Journal | Biochemistry |
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Year | 1991 |
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Volume | 30 |
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Pages | 4072-7 |
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Authors | Nishimura K, Tanizawa K, Yoshimura T, Esaki N, Futaki S, Manning JM, Soda K |
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Title | Effect of substitution of a lysyl residue that binds pyridoxal phosphate in thermostable D-amino acid aminotransferase by arginine and alanine. |
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[7] |
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PubMed ID | 1445909 |
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Journal | Biochemistry |
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Year | 1992 |
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Volume | 31 |
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Pages | 11748-54 |
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Authors | Yoshimura T, Bhatia MB, Manning JM, Ringe D, Soda K |
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Title | Partial reactions of bacterial D-amino acid transaminase with asparagine substituted for the lysine that binds coenzyme pyridoxal 5'-phosphate. |
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[8] |
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PubMed ID | 8463224 |
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Journal | J Biol Chem |
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Year | 1993 |
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Volume | 268 |
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Pages | 6932-8 |
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Authors | Bhatia MB, Futaki S, Ueno H, Manning JM, Ringe D, Yoshimura T, Soda K |
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Title | Kinetic and stereochemical comparison of wild-type and active-site K145Q mutant enzyme of bacterial D-amino acid transaminase. |
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[9] |
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Comments | X-RAY CRYSTALLOGRAPHY (1.94 ANGSTROMS) |
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Medline ID | 95352651 |
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PubMed ID | 7626635 |
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Journal | Biochemistry |
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Year | 1995 |
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Volume | 34 |
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Pages | 9661-9 |
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Authors | Sugio S, Petsko GA, Manning JM, Soda K, Ringe D |
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Title | Crystal structure of a D-amino acid aminotransferase: how the protein controls stereoselectivity. |
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Related PDB | 1daa |
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Related UniProtKB | P19938 |
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[10] |
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PubMed ID | 7592528 |
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Journal | J Biochem (Tokyo) |
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Year | 1995 |
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Volume | 117 |
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Pages | 691-6 |
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Authors | Kishimoto K, Yoshimura T, Esaki N, Sugio S, Manning JM, Soda K |
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Title | Role of leucine 201 of thermostable D-amino acid aminotransferase from a thermophile, Bacillus sp. YM-1. |
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[11] |
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PubMed ID | 8580849 |
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Journal | Protein Sci |
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Year | 1995 |
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Volume | 4 |
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Pages | 2578-86 |
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Authors | Van Ophem PW, Pospischil MA, Ringe D, Peisach D, Petsko G, Soda K, Manning JM |
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Title | Catalytic ability and stability of two recombinant mutants of D-amino acid transaminase involved in coenzyme binding. |
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[12] |
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PubMed ID | 8652553 |
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Journal | Biochemistry |
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Year | 1996 |
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Volume | 35 |
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Pages | 2112-6 |
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Authors | Martinez del Pozo A, van Ophem PW, Ringe D, Petsko G, Soda K, Manning JM |
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Title | Interaction of pyridoxal 5'-phosphate with tryptophan-139 at the subunit interface of dimeric D-amino acid transaminase. |
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[13] |
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PubMed ID | 9063963 |
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Journal | Biosci Biotechnol Biochem |
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Year | 1996 |
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Volume | 60 |
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Pages | 181-7 |
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Authors | Yoshimura T, Jhee KH, Soda K |
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Title | Stereospecificity for the hydrogen transfer and molecular evolution of pyridoxal enzymes. |
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[14] |
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PubMed ID | 9498563 |
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Journal | J Biochem (Tokyo) |
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Year | 1997 |
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Volume | 122 |
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Pages | 1182-9 |
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Authors | Kishimoto K, Yoshimura T, Soda K, Esaki N |
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Title | Mutation of arginine 98, which serves as a substrate-recognition site of D-amino acid aminotransferase, can be partly compensated for by mutation of tyrosine 88 to an arginyl residue. |
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[15] |
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PubMed ID | 9163511 |
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Journal | J Biochem (Tokyo) |
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Year | 1997 |
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Volume | 121 |
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Pages | 637-41 |
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Authors | Okada K, Hirotsu K, Sato M, Hayashi H, Kagamiyama H |
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Title | Three-dimensional structure of Escherichia coli branched-chain amino acid aminotransferase at 2.5 A resolution. |
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[16] |
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Comments | X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) |
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Medline ID | 98206914 |
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PubMed ID | 9538014 |
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Journal | Biochemistry |
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Year | 1998 |
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Volume | 37 |
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Pages | 4958-67 |
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Authors | Peisach D, Chipman DM, Van Ophem PW, Manning JM, Ringe D |
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Title | Crystallographic study of steps along the reaction pathway of D-amino acid aminotransferase. |
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Related PDB | 2daa,3daa,4daa |
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Related UniProtKB | P19938 |
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[17] |
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PubMed ID | 9914259 |
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Journal | Curr Opin Struct Biol |
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Year | 1998 |
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Volume | 8 |
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Pages | 759-69 |
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Authors | Jansonius JN |
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Title | Structure, evolution and action of vitamin B6-dependent enzymes. |
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[18] |
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PubMed ID | 9792912 |
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Journal | J Biochem (Tokyo) |
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Year | 1998 |
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Volume | 124 |
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Pages | 905-10 |
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Authors | Fuchikami Y, Yoshimura T, Gutierrez A, Soda K, Esaki N |
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Title | Construction and properties of a fragmentary D-amino acid aminotransferase. |
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[19] |
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Comments | X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) |
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Medline ID | 98420361 |
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PubMed ID | 9749913 |
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Journal | Protein Eng |
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Year | 1998 |
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Volume | 11 |
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Pages | 613-9 |
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Authors | Sugio S, Kashima A, Kishimoto K, Peisach D, Petsko GA, Ringe D, Yoshimura T, Esaki N |
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Title | Crystal structures of L201A mutant of D-amino acid aminotransferase at 2.0 A resolution: implication of the structural role of Leu201 in transamination. |
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Related PDB | 1a0g,2dab |
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Related UniProtKB | P19938 |
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[20] |
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Journal | J Microbiol Biotechnol |
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Year | 1999 |
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Volume | 9 |
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Pages | 695-703 |
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Authors | Jhee KH, Yoshimura T, Kurokawa Y, Esaki N, Soda K |
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Title | A stereochemical aspect of pyridoxal 5 '-phosphate dependent enzyme reactions and molecular evolution. |
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[21] |
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Comments | X-ray crystallography |
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PubMed ID | 9930994 |
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Journal | Biochemistry |
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Year | 1999 |
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Volume | 38 |
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Pages | 1323-31 |
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Authors | van Ophem PW, Peisach D, Erickson SD, Soda K, Ringe D, Manning JM |
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Title | Effects of the E177K mutation in D-amino acid transaminase. Studies on an essential coenzyme anchoring group that contributes to stereochemical fidelity. |
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Related PDB | 5daa |
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[22] |
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PubMed ID | 10800595 |
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Journal | Adv Enzymol Relat Areas Mol Biol |
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Year | 2000 |
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Volume | 74 |
---|
Pages | 129-84 |
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Authors | Mehta PK, Christen P |
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Title | The molecular evolution of pyridoxal-5'-phosphate-dependent enzymes. |
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[23] |
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PubMed ID | 10630999 |
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Journal | Biochemistry |
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Year | 2000 |
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Volume | 39 |
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Pages | 381-7 |
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Authors | Kishimoto K, Yasuda C, Manning JM |
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Title | Reversible dissociation/association of D-amino acid transaminase subunits: properties of isolated active dimers and inactive monomers. |
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[24] |
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PubMed ID | 11106434 |
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Journal | Eur J Biochem |
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Year | 2000 |
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Volume | 267 |
---|
Pages | 7218-23 |
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Authors | Gutierrez A, Yoshimura T, Fuchikami Y, Esaki N |
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Title | Modulation of activity and substrate specificity by modifying the backbone length of the distant interdomain loop of D-amino acid aminotransferase. |
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[25] |
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PubMed ID | 10673430 |
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Journal | Structure Fold Des |
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Year | 2000 |
---|
Volume | 8 |
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Pages | R1-6 |
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Authors | Schneider G, Kack H, Lindqvist Y |
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Title | The manifold of vitamin B6 dependent enzymes. |
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[26] |
---|
PubMed ID | 11933244 |
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Journal | Chem Rec |
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Year | 2001 |
---|
Volume | 1 |
---|
Pages | 373-84 |
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Authors | Soda K, Yoshimura T, Esaki N |
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Title | Stereospecificity for the hydrogen transfer of pyridoxal enzyme reactions. |
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[27] |
---|
PubMed ID | 11642362 |
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Journal | Prog Nucleic Acid Res Mol Biol |
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Year | 2001 |
---|
Volume | 70 |
---|
Pages | 175-206 |
---|
Authors | Hutson S |
---|
Title | Structure and function of branched chain aminotransferases. |
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[28] |
---|
PubMed ID | 12297014 |
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Journal | J Biochem Mol Biol |
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Year | 2002 |
---|
Volume | 35 |
---|
Pages | 306-12 |
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Authors | Ro HS |
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Title | Effects of salts on the conformation and catalytic properties of d-amino acid aminotransferase. |
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comments | This enzyme belongs to the fold-type IV pyridoxal-phosphate-dependent enzymes (see [17]). Unlike other PLP-dependent aminotransferases (D00101, D00102 in EzCatDB), the catalytic lysine (Lus145) of this enzyme transfer the pro-R hydrogen at the C4' position of pyridoxal phosphate (PLP) on the re face (see [9], [13]). However, the catalytic residues surrounding PLP of this enzyme is very similar to that of aspartate aminotransferase (D00101 in EzCatDB), according to the literature [15]. This enzyme catalyzes transamination, which is composed of the following reactions (see [16]): (A) Formation of external aldimine (with amine group of D-alanine). (B) Isomerization (change in the position of double-bond), forming a ketimine intermediate. (C) Schiff-base deforming by hydration, releasing the first product, pyruvate, and PMP. (D) Schiff-base forming of PMP with carbonyl group of the second substrate, 2-oxoglutarate, leaging again to a ketimine intermediate. (E) Isomerization (change in the position of double-bond). (F) Formation of internal aldimine, leading to the elimination of the product, D-glutamate, from PLP. These reactions proceed in the following way: (A) Formation of external aldimine (with amine group of D-alanine). (A1) Tyr31 might interact with O3' atom of PLP through a water together with the imine nitrogen of Lys145, when the PLP-aldimine is protonated, modulating and keeping the O3' of PLP negatively charged (see [15], [16]). (A2) The negatively charged O3' atom of PLP modulates the pKa of the internal aldimine with Lys145 (see [16]). (A3) The deprotonated amine group of D-alanine makes a nucleophilic attack on the C4' carbon of PLP, forming a transient geminal diamine intermediate (see [16]). (A4) There must be a general base, which deprotonates the amine group of the previously D-alanine substrate, so that the lone pair of the amine group can attack on the C4' atom to form a double-bond, and to release the amine of the catalytic residue, Lys145. The adjacent Lys145 nitrogen may act as a general base to deprotonate the amine group of the incoming substrate, through a water molecule. (see [16]) (A5) The reaction produces the external aldimine with D-alanine. (B) Isomerization (change in the position of double-bond), forming a ketimine intermediate. (B1) Glu177 interacts with the N1 atom of PLP, keeping the protonated state of the pyridinium nitrogen of PLP, so that it can modulate and enhance the activity of the PLP cofactor as an electron sink, which facilitates the abstraction of alpha-proton from the D-alanine covalently bound to the PLP (see [16] & [21]). At the same time, Tyr31 seems to modulate the pKa of Lys145 sidechain, whereas the O3' atom of PLP interacts with the Schiff-base nitrogen atom, modulating its pKa (see [16]). (B2) Lys145 acts as a general base to deprotonate the alpha-proton of the amino acid substrate, forming a quinonoid intermediate. (B3) Lys145 acts as a general acid to protonate the C4' atom of the PLP, leading to the formation of a ketimine intermediate. (C) Schiff-base deforming by hydration, releasing the first product, pyruvate, and PMP. (C0) Considering the active site of enzyme (PDB;2daa), a water molecule is unlikely to approach from the side of the active site residues, Tyr31 and Lys145. (C1) Thus, His100* from the adjacent subunit might act as a general base to activate the water molecule at the si-face side of cofactor. (C2) The activated water molecule makes a nucleophilic attack on the alpha-carbon atom of the substrate (from the si-face side), forming a carbinolamine intermediate. (C3) The protonated His100* might transfer the proton to Lys145, through a water molecule and either O3' atom of PLP or Tyr31. (C4) Lys145 may act as a general acid to protonate the N4' atom of the PLP. Tyr31 may modulate the activity of Lys145. (C5) The lone pair of the hydroxyl oxygen makes a nucleophilic attack on the C4' atom, whereas His100* acts as a general base to deprotonate the hydroxyl group. (C6) The protonated His100* might transfer the proton to Lys145, through a water molecule and either O3' atom of PLP or Tyr31. Finally, Lys145 act as a general acid to protonate the N4' atom, releasing the first product, pyruvate and the PMP. (D) Schiff-base forming of PMP with carbonyl group of the second substrate, 2-oxoglutarate. (D0) The second substrate, 2-oxoglutarate, is bound to the active site, with the carbonyl oxygen hydrogen-bonded by His100*. (D1) Lys145 acts as a general base to deprotonate the amine group (or the N4' atom) of PMP. (D2) The deprotonated amine group (or the N4' atom) of PMP makes a nucleophilic attack on the carbonyl carbon of the substrate, whereas His100* acts as a general acid to protonate the carbonyl oxygen, forming a carbinolamine intermediate. (D3) The protonated Lys145 might transfer the proton to His100*, through a water molecule and either O3' atom of PLP or Tyr31. (D4) Lys145 acts as a general base to deprotonate the N4' amine group. Tyr31 may modulate the activity of Lys258. (D5) The lone pair of the N4' nitrogen atom makes a nucleophilic attack on the carbon atom, whereas His100* acts as a general acid to the hydroxyl group of the carbinolamine intermediate, leading to the cleavage between the carbon and the N4' atom, and to the release of a water moleucle. This reaction gives a ketimine intermediate again. (E) Isomerization (change in the position of double-bond). (E1) Glu177 modulates and enhances the activity of the PLP cofactor as an electron sink, which facilitates the abstraction of alpha-proton from the C4' atom of the PLP. At the same time, Tyr31 seems to modulate the pKa of Lys145 sidechain, whereas the O3' atom of PLP interacts with the Schiff-base nitrogen atom, modulating the pKa (see [16]). (E2) Lys145 acts as a general base to deprotonate the C4' atom of the PLP, leading to the formation of a quinonoid intermediate. (E3) Lys145 acts as a general acid to protonate the alpha-proton of the amino acid substrate, forming an external aldimine. (As a result, Lys145 must be deprotonated, so that it can act as a general base at the next stage.) (F) Formation of internal aldimine, leading to the elimination of the product, D-glutamate, from PLP. (F1) Tyr31 might interact with O3' atom of PLP through a water , when the PLP-aldimine is protonated, modulating and keeping the O3' of PLP negatively charged (see [15], [16]). (F2) The negatively charged O3' atom of PLP modulates the pKa of the internal aldimine with Lys145 (see [16]). (F3) The deprotonated amine group of Lys145 makes a nucleophilic attack on the C4' carbon of the PLP of the external aldimine, forming a transient geminal diamine intermediate. (F4) There must be a general acid, which protonates the N4' nitrogen atom of the external aldimine or the geminal diamine. Considering the active-site structure, The adjacent Lys145 nitrogen may play the role as the general acid to protonate the N4' atom, through a water. (F5) The lone pair of the amine nitrogen of Lys145 can attack on the C4' atom to form a double-bond, and to release the amine of the second product, D-glutamate.
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2004-03-18 | 2009-02-26 |
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