|
KEGG pathways | MAP code | Pathways |
---|
MAP00252 | Alanine and aspartate metabolism | MAP00473 | D-Alanine metabolism |
UniProtKB:Accession Number | P10724 | Q9HTQ2 | Q65YW7 | P0A4X2 |
---|
Entry name | ALR_BACST | ALR2_PSEAE | Q65YW7_STRLA | ALR_MYCTU |
---|
Activity | L-alanine = D-alanine. | L-alanine = D-alanine. | L-alanine = D-alanine. | L-alanine = D-alanine. |
---|
Subunit | Homodimer. |
|
|
|
---|
Subcellular location |
|
|
|
|
---|
Cofactor | Pyridoxal phosphate. | Pyridoxal phosphate (By similarity). | Pyridoxal phosphate.,Pyridoxal phosphate (By similarity). | Pyridoxal phosphate (By similarity). |
---|
Compound table: links to PDB-related databases & PoSSuM |
---|
| Cofactors | Substrates | Products | intermediates |
---|
KEGG-id | C00018 | C00041 | C00133 | I00049 | I00032 | I00029 |
---|
Compound | Pyridoxal phosphate | L-Alanine | D-Alanine | External aldimine intermediate (initial stage:PLP-L-Ala) | Quinonoid intermediate (PLP-Ala) | External aldimine intermediate (final stage:PLP-D-Ala) |
---|
Type | aromatic ring (with nitrogen atoms),phosphate group/phosphate ion | amino acids | amino acids |
|
|
|
---|
ChEBI | 18405
| 16977 57972
| 15570 57416
|
|
|
|
---|
PubChem | 1051
| 7311724 5950
| 7311725 71080
|
|
|
|
---|
| | | | | | | | | | | | | |
---|
1bd0A01 |  |  |  |  |  |  |  | Analogue:IN5 | Unbound | Unbound | Intermediate-analogue:IN5 | Unbound | Unbound |
---|
1bd0B01 |  |  |  |  |  |  |  | Analogue:IN5 | Unbound | Unbound | Intermediate-analogue:IN5 | Unbound | Unbound |
---|
1epvA01 |  |  |  |  |  |  |  | Analogue:DCS | Unbound | Unbound | Unbound | Intermediate-analogue:DCS | Unbound |
---|
1epvB01 |  |  |  |  |  |  |  | Analogue:DCS | Unbound | Unbound | Unbound | Intermediate-analogue:DCS | Unbound |
---|
1ftxA01 |  |  |  |  |  |  |  | Analogue:EPC | Unbound | Unbound | Unbound | Unbound | Intermediate-analogue:EPC |
---|
1ftxB01 |  |  |  |  |  |  |  | Analogue:EPC | Unbound | Unbound | Unbound | Unbound | Intermediate-analogue:EPC |
---|
1l6fA01 |  |  |  |  |  |  |  | Analogue:PP3 | Unbound | Unbound | Intermediate-bound:PP3 | Unbound | Unbound |
---|
1l6fB01 |  |  |  |  |  |  |  | Analogue:PP3 | Unbound | Unbound | Intermediate-bound:PP3 | Unbound | Unbound |
---|
1l6gA01 |  |  |  |  |  |  |  | Analogue:PDD | Unbound | Unbound | Unbound | Unbound | Intermediate-bound:PDD |
---|
1l6gB01 |  |  |  |  |  |  |  | Analogue:PDD | Unbound | Unbound | Unbound | Unbound | Intermediate-bound:PDD |
---|
1niuA01 |  |  |  |  |  |  |  | Analogue:DCS | Unbound | Unbound | Unbound | Intermediate-analogue:DCS | Unbound |
---|
1niuB01 |  |  |  |  |  |  |  | Analogue:DCS | Unbound | Unbound | Unbound | Intermediate-analogue:DCS | Unbound |
---|
1sftA01 |  |  |  |  |  |  |  | Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1sftB01 |  |  |  |  |  |  |  | Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1xqkA01 |  |  |  |  |  |  |  | Analogue:PMH | Unbound | Unbound | Unbound | Intermediate-analogue:PMH | Unbound |
---|
1xqkB01 |  |  |  |  |  |  |  | Analogue:PMH | Unbound | Unbound | Unbound | Intermediate-analogue:PMH | Unbound |
---|
1xqlA01 |  |  |  |  |  |  |  | Analogue:PLP-PMH-PMP | Unbound | Unbound | Unbound | Intermediate-analogue:PMH | Intermediate-analogue:PMP-4AX |
---|
1xqlB01 |  |  |  |  |  |  |  | Analogue:PLP-PMH-PMP | Unbound | Unbound | Unbound | Intermediate-analogue:PMH | Intermediate-analogue:PMP-4AX |
---|
2sfpA01 |  |  |  |  |  |  |  | Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
2sfpB01 |  |  |  |  |  |  |  | Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1rcqA01 |  |  |  |  |  |  |  | Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1vfhA01 |  |  |  |  |  |  |  | Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1vfsA01 |  |  |  |  |  |  |  | Analogue:DCS | Unbound | Unbound | Unbound | Intermediate-analogue:DCS | Unbound |
---|
1vfsB01 |  |  |  |  |  |  |  | Analogue:DCS | Unbound | Unbound | Unbound | Intermediate-analogue:DCS | Unbound |
---|
1vftA01 |  |  |  |  |  |  |  | Analogue:DCS | Unbound | Unbound | Unbound | Intermediate-analogue:DCS | Unbound |
---|
1vftB01 |  |  |  |  |  |  |  | Analogue:DCS | Unbound | Unbound | Unbound | Intermediate-analogue:DCS | Unbound |
---|
1xfcA01 |  |  |  |  |  |  |  | Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1xfcB01 |  |  |  |  |  |  |  | Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1bd0A02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1bd0B02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1epvA02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1epvB02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1ftxA02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1ftxB02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1l6fA02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1l6fB02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1l6gA02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1l6gB02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1niuA02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1niuB02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1sftA02 |  |  |  |  |  |  |  | Unbound | Analogue:ACT | Unbound | Unbound | Unbound | Unbound |
---|
1sftB02 |  |  |  |  |  |  |  | Unbound | Analogue:ACT | Unbound | Unbound | Unbound | Unbound |
---|
1xqkA02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1xqkB02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1xqlA02 |  |  |  |  |  |  |  | Unbound | Analogue:ACY | Unbound | Unbound | Unbound | Unbound |
---|
1xqlB02 |  |  |  |  |  |  |  | Unbound | Analogue:ACY | Unbound | Unbound | Unbound | Unbound |
---|
2sfpA02 |  |  |  |  |  |  |  | Unbound | Analogue:PPI | Unbound | Unbound | Unbound | Unbound |
---|
2sfpB02 |  |  |  |  |  |  |  | Unbound | Analogue:PPI | Unbound | Unbound | Unbound | Unbound |
---|
1rcqA02 |  |  |  |  |  |  |  | Unbound | Unbound | Analogue:DLY | Unbound | Unbound | Unbound |
---|
1vfhA02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1vfsA02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1vfsB02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1vftA02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1vftB02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1xfcA02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
1xfcB02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
---|
References for Catalytic Mechanism | References | Sections | No. of steps in catalysis |
---|
[8] | Fig.7, p.1334-1341 |
| [9] | Scheme 1, p.10441-10443 |
| [10] | p.3295-3300 |
| [11] | Scheme 1, Scheme 2, p.4064-4065 |
| [12] | Fig.1 |
| [13] | Fig.1 |
| [14] | Scheme I, Scheme II, p.4193-4194 |
| [17] | p.2832-3834 |
| [18] | Scheme I, Scheme II, p.19169-10172 |
| [21] | Fig.5, p.5104-5107 |
| [27] | Fig 9, Fig.11, p.284-286 |
|
references | [1] |
---|
PubMed ID | 7034778 |
---|
Journal | Biochemistry |
---|
Year | 1981 |
---|
Volume | 20 |
---|
Pages | 7539-46 |
---|
Authors | Wang EA, Walsh C |
---|
Title | Characteristics of beta, beta-difluoroalanine and beta, beta, beta -trifluoroalanine as suicide substrates for Escherichia coli B alanine racemase. |
---|
[2] |
---|
PubMed ID | 6427785 |
---|
Journal | Prog Clin Biol Res |
---|
Year | 1984 |
---|
Volume | 144A |
---|
Pages | 339-50 |
---|
Authors | Johnston RB, Schreiber EC, Davis MP, Jillson L, Sorrell WT, Kirker ME |
---|
Title | Catalytic properties of the active site of alanine racemase from B. subtilis. |
---|
[3] |
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PubMed ID | 3730360 |
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Journal | Biochemistry |
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Year | 1986 |
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Volume | 25 |
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Pages | 3275-82 |
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Authors | Badet B, Inagaki K, Soda K, Walsh CT |
---|
Title | Time-dependent inhibition of Bacillus stearothermophilus alanine racemase by (1-aminoethyl)phosphonate isomers by isomerization to noncovalent slowly dissociating enzyme-(1-aminoethyl)phosphonate complexes. |
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[4] |
---|
PubMed ID | 3118951 |
---|
Journal | Biochemistry |
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Year | 1987 |
---|
Volume | 26 |
---|
Pages | 5878-84 |
---|
Authors | Mobashery S, Johnston M |
---|
Title | Inactivation of alanine racemase by beta-chloro-L-alanine released enzymatically from amino acid and peptide C10-esters of deacetylcephalothin. |
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[5] |
---|
PubMed ID | 3680197 |
---|
Journal | J Biol Chem |
---|
Year | 1987 |
---|
Volume | 262 |
---|
Pages | 15323-6 |
---|
Authors | Neidhart DJ, Distefano MD, Tanizawa K, Soda K, Walsh CT, Petsko GA |
---|
Title | X-ray crystallographic studies of the alanine-specific racemase from Bacillus stearothermophilus. Overproduction, crystallization, and preliminary characterization. |
---|
[6] |
---|
PubMed ID | 3167024 |
---|
Journal | Biochemistry |
---|
Year | 1988 |
---|
Volume | 27 |
---|
Pages | 4966-70 |
---|
Authors | Copie V, Faraci WS, Walsh CT, Griffin RG |
---|
Title | Inhibition of alanine racemase by alanine phosphonate: detection of an imine linkage to pyridoxal 5'-phosphate in the enzyme-inhibitor complex by solid-state 15N nuclear magnetic resonance. |
---|
[7] |
---|
PubMed ID | 2690935 |
---|
Journal | Biochemistry |
---|
Year | 1989 |
---|
Volume | 28 |
---|
Pages | 8167-74 |
---|
Authors | Galakatos NG, Walsh CT |
---|
Title | Mutations at the interdomain hinge region of the DadB alanine racemase: effects of length and conformational constraint of the linker sequence on catalytic efficiency. |
---|
[8] |
---|
Comments | X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS), AND REVISIONS. |
---|
Medline ID | 97178818 |
---|
PubMed ID | 9063881 |
---|
Journal | Biochemistry |
---|
Year | 1997 |
---|
Volume | 36 |
---|
Pages | 1329-42 |
---|
Authors | Shaw JP, Petsko GA, Ringe D |
---|
Title | Determination of the structure of alanine racemase from Bacillus stearothermophilus at 1.9-A resolution. |
---|
Related PDB | 1sft |
---|
Related UniProtKB | P10724 |
---|
[9] |
---|
Comments | X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS). |
---|
Medline ID | 98337786 |
---|
PubMed ID | 9671513 |
---|
Journal | Biochemistry |
---|
Year | 1998 |
---|
Volume | 37 |
---|
Pages | 10438-45 |
---|
Authors | Stamper GF, Morollo AA, Ringe D, Stamper CG |
---|
Title | Reaction of alanine racemase with 1-aminoethylphosphonic acid forms a stable external aldimine. |
---|
Related PDB | 1bd0 |
---|
Related UniProtKB | P10724 |
---|
[10] |
---|
Comments | X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS). |
---|
Medline ID | 99178834 |
---|
PubMed ID | 10079072 |
---|
Journal | Biochemistry |
---|
Year | 1999 |
---|
Volume | 38 |
---|
Pages | 3293-301 |
---|
Authors | Morollo AA, Petsko GA, Ringe D |
---|
Title | Structure of a Michaelis complex analogue: propionate binds in the substrate carboxylate site of alanine racemase. |
---|
Related PDB | 2sfp |
---|
Related UniProtKB | P10724 |
---|
[11] |
---|
Comments | MUTAGENESIS OF ARG-219. |
---|
Medline ID | 99212226 |
---|
PubMed ID | 10194319 |
---|
Journal | Biochemistry |
---|
Year | 1999 |
---|
Volume | 38 |
---|
Pages | 4058-65 |
---|
Authors | Sun S, Toney MD |
---|
Title | Evidence for a two-base mechanism involving tyrosine-265 from arginine-219 mutants of alanine racemase. |
---|
Related UniProtKB | P10724 |
---|
[12] |
---|
PubMed ID | 10348897 |
---|
Journal | J Biochem (Tokyo) |
---|
Year | 1999 |
---|
Volume | 125 |
---|
Pages | 987-90 |
---|
Authors | Watanabe A, Kurokawa Y, Yoshimura T, Esaki N |
---|
Title | Role of tyrosine 265 of alanine racemase from Bacillus stearothermophilus. |
---|
[13] |
---|
Comments | ACTIVE SITES, AND MUTAGENESIS. |
---|
Medline ID | 99434146 |
---|
PubMed ID | 10502689 |
---|
Journal | J Biochem (Tokyo) |
---|
Year | 1999 |
---|
Volume | 126 |
---|
Pages | 781-6 |
---|
Authors | Watanabe A, Yoshimura T, Mikami B, Esaki N |
---|
Title | Tyrosine 265 of alanine racemase serves as a base abstracting alpha-hydrogen from L-alanine: the counterpart residue to lysine 39 specific to D-alanine. |
---|
Related UniProtKB | P10724 |
---|
[14] |
---|
PubMed ID | 9933615 |
---|
Journal | J Biol Chem |
---|
Year | 1999 |
---|
Volume | 274 |
---|
Pages | 4189-94 |
---|
Authors | Watanabe A, Kurokawa Y, Yoshimura T, Kurihara T, Soda K, Esaki N, Watababe A |
---|
Title | Role of lysine 39 of alanine racemase from Bacillus stearothermophilus that binds pyridoxal 5'-phosphate. Chemical rescue studies of Lys39 --> Ala mutant. |
---|
[15] |
---|
PubMed ID | 11064190 |
---|
Journal | FEMS Microbiol Lett |
---|
Year | 2000 |
---|
Volume | 192 |
---|
Pages | 169-73 |
---|
Authors | Okubo Y, Yokoigawa K, Esaki N, Soda K, Misono H |
---|
Title | High catalytic activity of alanine racemase from psychrophilic Bacillus psychrosaccharolyticus at high temperatures in the presence of pyridoxal 5'-phosphate. |
---|
[16] |
---|
PubMed ID | 10673430 |
---|
Journal | Structure Fold Des |
---|
Year | 2000 |
---|
Volume | 8 |
---|
Pages | R1-6 |
---|
Authors | Schneider G, Kack H, Lindqvist Y |
---|
Title | The manifold of vitamin B6 dependent enzymes. |
---|
[17] |
---|
PubMed ID | 11456969 |
---|
Journal | J Am Chem Soc |
---|
Year | 2001 |
---|
Volume | 123 |
---|
Pages | 2830-4 |
---|
Authors | Ondrechen MJ, Briggs JM, McCammon JA |
---|
Title | A model for enzyme-substrate interaction in alanine racemase. |
---|
[18] |
---|
Comments | X-ray crystallography |
---|
PubMed ID | 11886871 |
---|
Journal | J Biol Chem |
---|
Year | 2002 |
---|
Volume | 277 |
---|
Pages | 19166-72 |
---|
Authors | Watanabe A, Yoshimura T, Mikami B, Hayashi H, Kagamiyama H, Esaki N |
---|
Title | Reaction mechanism of alanine racemase from Bacillus stearothermophilus: x-ray crystallographic studies of the enzyme bound with N-(5'-phosphopyridoxyl)alanine. |
---|
Related PDB | 1l6f,1l6g |
---|
[19] |
---|
Comments | X-ray crystallography |
---|
PubMed ID | 12741835 |
---|
Journal | Biochemistry |
---|
Year | 2003 |
---|
Volume | 42 |
---|
Pages | 5775-83 |
---|
Authors | Fenn TD, Stamper GF, Morollo AA, Ringe D |
---|
Title | A side reaction of alanine racemase: transamination of cycloserine. |
---|
Related PDB | 1epv,1niu |
---|
[20] |
---|
PubMed ID | 14674749 |
---|
Journal | Biochemistry |
---|
Year | 2003 |
---|
Volume | 42 |
---|
Pages | 14752-61 |
---|
Authors | LeMagueres P, Im H, Dvorak A, Strych U, Benedik M, Krause KL |
---|
Title | Crystal structure at 1.45 A resolution of alanine racemase from a pathogenic bacterium, Pseudomonas aeruginosa, contains both internal and external aldimine forms. |
---|
Related PDB | 1rcq |
---|
[21] |
---|
PubMed ID | 12718553 |
---|
Journal | Biochemistry |
---|
Year | 2003 |
---|
Volume | 42 |
---|
Pages | 5099-107 |
---|
Authors | Spies MA, Toney MD |
---|
Title | Multiple hydrogen kinetic isotope effects for enzymes catalyzing exchange with solvent: application to alanine racemase. |
---|
[22] |
---|
PubMed ID | 12686135 |
---|
Journal | Biochim Biophys Acta |
---|
Year | 2003 |
---|
Volume | 1647 |
---|
Pages | 214-9 |
---|
Authors | Paiardini A, Contestabile R, D'Aguanno S, Pascarella S, Bossa F |
---|
Title | Threonine aldolase and alanine racemase: novel examples of convergent evolution in the superfamily of vitamin B6-dependent enzymes. |
---|
[23] |
---|
PubMed ID | 14517907 |
---|
Journal | Biopolymers |
---|
Year | 2003 |
---|
Volume | 70 |
---|
Pages | 186-200 |
---|
Authors | Mustata GI, Soares TA, Briggs JM |
---|
Title | Molecular dynamics studies of alanine racemase: a structural model for drug design. |
---|
[24] |
---|
PubMed ID | 12725937 |
---|
Journal | FEMS Microbiol Lett |
---|
Year | 2003 |
---|
Volume | 221 |
---|
Pages | 263-7 |
---|
Authors | Yokoigawa K, Okubo Y, Soda K |
---|
Title | Subunit interaction of monomeric alanine racemases from four Shigella species in catalytic reaction. |
---|
[25] |
---|
PubMed ID | 15302886 |
---|
Journal | J Biol Chem |
---|
Year | 2004 |
---|
Volume | 279 |
---|
Pages | 46153-61 |
---|
Authors | Noda M, Matoba Y, Kumagai T, Sugiyama M |
---|
Title | Structural evidence that alanine racemase from a D-cycloserine-producing microorganism exhibits resistance to its own product. |
---|
Related PDB | 1vfh,1vfs,1vft |
---|
[26] |
---|
PubMed ID | 15115851 |
---|
Journal | Protein Eng Des Sel |
---|
Year | 2004 |
---|
Volume | 17 |
---|
Pages | 223-34 |
---|
Authors | Mustata G, Briggs JM |
---|
Title | Cluster analysis of water molecules in alanine racemase and their putative structural role. |
---|
[27] |
---|
PubMed ID | 15581583 |
---|
Journal | Arch Biochem Biophys |
---|
Year | 2005 |
---|
Volume | 433 |
---|
Pages | 279-87 |
---|
Authors | Toney MD |
---|
Title | Reaction specificity in pyridoxal phosphate enzymes. |
---|
[28] |
---|
Comments | X-ray crystallography |
---|
PubMed ID | 15807525 |
---|
Journal | Biochemistry |
---|
Year | 2005 |
---|
Volume | 44 |
---|
Pages | 5317-27 |
---|
Authors | Fenn TD, Holyoak T, Stamper GF, Ringe D |
---|
Title | Effect of a Y265F Mutant on the Transamination-Based Cycloserine Inactivation of Alanine Racemase. |
---|
Related PDB | 1xqk,1xql |
---|
[29] |
---|
PubMed ID | 15683232 |
---|
Journal | Biochemistry |
---|
Year | 2005 |
---|
Volume | 44 |
---|
Pages | 1471-81 |
---|
Authors | LeMagueres P, Im H, Ebalunode J, Strych U, Benedik MJ, Briggs JM, Kohn H, Krause KL |
---|
Title | The 1.9 A crystal structure of alanine racemase from Mycobacterium tuberculosis contains a conserved entryway into the active site. |
---|
Related PDB | 1xfc |
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comments | This enzyme belongs to the type-III PLP-dependent enzyme superfamily. This enzyme catalyzes racemization, which is composed of the following reactions (see [8], [11], [14], [18], [21] & [27]): (A) Formation of an external aldimine (with amine group of L-Ala, PLP-L-Ala; I00049): (B) Isomerization (change in the position of double-bond), forming a quinonoid intermediate (PLP-Ala; I00032). (C) Isomerization (change in the position of double-bond), forming an external aldimine (PLP-D-Ala; I00029). (D) Formation of internal aldimine, leading to the release of the product from PLP. These reactions proceed in the following way: (A) Formation of external aldimine (PLP-L-Ala; I00049) (see [8], [11], [14], [18], [21] & [27]); (A1) The interaction of Arg219 through His166 with Tyr265' (from the adjacent chain) keeps the sidechain of Tyr265' unprotonated. (Arg219/His166 act as modulators.) In addition, Asp313' may modulate the activity of Lys39. (A2) Tyr265' acts as a general base to deprotonate and activate the protonated amine group of substrate, L-Ala. (A3) The deprotonated amine group of L-Ala makes a nucleophilic attack on the C4' atom of PLP, which forms an internal aldimine with Lys39, forming a transient geminal diamine intermediate. (A4) Proton transfer from the amine group of L-Ala to epsilon-nitrogen atom of Lys39 must occur (probably through alpha-carboxyl group, or C4' atom of PLP). (A5) The lone pair of the amine group of L-Ala makes the second nucleophilic attack on the C4' atom, leading to the formation of the external aldimine with L-Ala and the release of Lys39 (unprotonated). (B) Isomerization (change in the position of double-bond), forming a quinonoid intermediate (PLP-Ala; I00032) (see [8], [11], [14], [18], [21] & [27]); (B1) Protonated Tyr265' must be deprotonated, whereas unprotonated Lys39 must be protonated. Here, alpha-carboxyl group of L-Ala=PLP might acts as a base-acid, which deprotonates the sidechain of Tyr265' and protonates that of Lys39 (see [18]). Here, Arg219/His166 may modulate the activity of Tyr265'. (B2) Tyr265' acts as a general base to deprotonate the alpha-proton of the L-amino acid substrate, forming a quinonoid intermediate (or carbanion intermediate). (B3) Arg219 interacts with the N1 atom of PLP, modulating and decreasing (or destabilizing) the activity of the PLP cofactor as an electron sink, which destabilizes quinonoid intermediate and facilitates the next step of reprotonation of alpha-carbon (see [8]). (C) Isomerization (change in the position of double-bond), forming an external aldimine (PLP-D-Ala; I00029): (Inverse reaction of (B)) (C1) Arg219 interacts with the N1 atom of PLP, modulating and decreasing (or destabilizing) the activity of the PLP cofactor as an electron sink, which destabilizes quinonoid intermediate and facilitates the this step. In addition, Asp313' may modulate the activity of Lys39. (C2) Lys39 acts as a general acid to protonate the alpha-carbon of the L-amino acid substrate from the opposite side of Tyr265' (from re face of PLP). This reaction leads to the formation of the external aldimine of D-Ala with PLP. (D) Formation of internal aldimine, leading to the elimination of the product from PLP: (Inverse reaction of (A)); (D1) Asp313' may modulate the activity of Lys39. (D2) The deprotonated amine group of Lys39 makes a nucleophilic attack on the C4' carbon of the PLP of the external aldimine, forming a transient geminal diamine intermediate. (D2) Proton transfer from the epsilon-nitrogen atom of Lys39 to the amine group of D-Ala must occur (probably through alpha-carboxyl group, or C4' atom of PLP). (D3) The lone pair of the amine nitrogen of Lys39 can attack on the C4' atom to form a double-bond, and to release the amine of the product, D-Ala. (D4) The interaction of Arg219 through His166 with Tyr265' (from the adjacent chain) assists Tyr265' in acting as a general acid to protonate the amine group of the product. (Arg219/His166 act as modulators.)
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2005-04-18 | 2015-07-23 |
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