DB code: D00271
| RLCP classification | 6.30.93020.5311 : Double-bonded atom exchange | |
|---|---|---|
| 8.12111.792000.5722 : Isomerization | ||
| 8.11211.912000.5525 : Isomerization | ||
| 6.40.508000.5522 : Double-bonded atom exchange | ||
| CATH domain | 3.20.20.10 : TIM Barrel | Catalytic domain |
| 2.40.37.10 : Lyase, Ornithine Decarboxylase; Chain A, domain 1 | Catalytic domain | |
| E.C. | 5.1.1.1 | |
| CSA | 1bd0 | |
| M-CSA | 1bd0 | |
| MACiE | M0213 | |
| CATH domain | Related DB codes (homologues) |
|---|---|
| 2.40.37.10 : Lyase, Ornithine Decarboxylase; Chain A, domain 1 | D00251 |
| 3.20.20.10 : TIM Barrel | D00251 |
| Uniprot Enzyme Name | UniprotKB | Protein name | Synonyms | Pfam | RefSeq |
|---|---|---|---|---|
| P10724 |
Alanine racemase
|
EC
5.1.1.1
|
PF00842
(Ala_racemase_C)
PF01168 (Ala_racemase_N) [Graphical View] |
|
| Q9HTQ2 |
Alanine racemase, catabolic
|
EC
5.1.1.1
|
PF00842
(Ala_racemase_C)
PF01168 (Ala_racemase_N) [Graphical View] |
NP_253989.1
(Protein)
NC_002516.2 (DNA/RNA sequence) |
| Q65YW7 |
Alanine racemase
|
EC
5.1.1.1
|
PF00842
(Ala_racemase_C)
PF01168 (Ala_racemase_N) [Graphical View] |
|
| P0A4X2 |
Alanine racemase
|
EC
5.1.1.1
|
PF00842
(Ala_racemase_C)
PF01168 (Ala_racemase_N) [Graphical View] |
NP_217940.1
(Protein)
NC_000962.3 (DNA/RNA sequence) NP_338056.1 (Protein) NC_002755.2 (DNA/RNA sequence) YP_006516909.1 (Protein) NC_018143.1 (DNA/RNA sequence) |
| KEGG enzyme name |
|---|
|
alanine racemase
L-alanine racemase |
| UniprotKB: Accession Number | Entry name | Activity | Subunit | Subcellular location | Cofactor |
|---|---|---|---|---|---|
| P10724 | ALR_BACST | L-alanine = D-alanine. | Homodimer. | Pyridoxal phosphate. | |
| Q9HTQ2 | ALR2_PSEAE | L-alanine = D-alanine. | Pyridoxal phosphate (By similarity). | ||
| Q65YW7 | Q65YW7_STRLA | L-alanine = D-alanine. | Pyridoxal phosphate. Pyridoxal phosphate (By similarity). | ||
| P0A4X2 | ALR_MYCTU | L-alanine = D-alanine. | Pyridoxal phosphate (By similarity). |
| KEGG Pathways | Map code | Pathways | E.C. |
|---|---|---|
| MAP00252 | Alanine and aspartate metabolism | |
| MAP00473 | D-Alanine metabolism |
| Compound table | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Cofactors | Substrates | Products | Intermediates | ||||||||
| KEGG-id | C00018 | C00041 | C00133 | I00049 | I00032 | I00029 | |||||
| E.C. | |||||||||||
| 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 18405 |
16977 57972 16977 57972 |
15570 57416 15570 57416 |
||||||||
| PubChem |
1051 1051 |
5950 7311724 5950 7311724 |
71080 7311725 71080 7311725 |
||||||||
| 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 |
| Reference for Active-site residues | ||
|---|---|---|
| resource | references | E.C. |
| Swiss-prot;P10724 & literature [18] | ||
| Active-site residues | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| PDB | Catalytic residues | Cofactor-binding residues | Modified residues | Main-chain involved in catalysis | Comment | |||||
| 1bd0A01 |
|
|
|
|
|
LYS 39;HIS 166;ARG 219 | LYS 39(PLP binding) | |||
| 1bd0B01 |
|
|
|
|
|
LYS 39;HIS 166;ARG 219 | LYS 39(PLP binding) | |||
| 1epvA01 |
|
|
|
|
|
LYS 39;HIS 166;ARG 219 | LYS 39(PLP binding) | KCX 129(carbamylated Lys) | ||
| 1epvB01 |
|
|
|
|
|
LYS 39;HIS 166;ARG 219 | LYS 39(PLP binding) | KCX 129(carbamylated Lys) | ||
| 1ftxA01 |
|
|
|
|
|
LYS 39;HIS 166;ARG 219 | LYS 39(PLP binding) | KCX 129(carbamylated Lys) | ||
| 1ftxB01 |
|
|
|
|
|
LYS 39;HIS 166;ARG 219 | LYS 39(PLP binding) | KCX 129(carbamylated Lys) | ||
| 1l6fA01 |
|
|
|
|
|
LYS 39;HIS 166;ARG 219 | LYS 39(PLP binding) | KCX 129(carbamylated Lys) | ||
| 1l6fB01 |
|
|
|
|
|
LYS 39;HIS 166;ARG 219 | LYS 39(PLP binding) | KCX 129(carbamylated Lys) | ||
| 1l6gA01 |
|
|
|
|
|
LYS 39;HIS 166;ARG 219 | LYS 39(PLP binding) | KCX 129(carbamylated Lys) | ||
| 1l6gB01 |
|
|
|
|
|
LYS 39;HIS 166;ARG 219 | LYS 39(PLP binding) | KCX 129(carbamylated Lys) | ||
| 1niuA01 |
|
|
|
|
|
LYS 39;HIS 166;ARG 219 | LYS 39(PLP binding) | KCX 129(carbamylated Lys) | ||
| 1niuB01 |
|
|
|
|
|
LYS 39;HIS 166;ARG 219 | LYS 39(PLP binding) | KCX 129(carbamylated Lys) | ||
| 1sftA01 |
|
|
|
|
|
LYS 39;HIS 166;ARG 219 | LYS 39(PLP binding) | |||
| 1sftB01 |
|
|
|
|
|
LYS 39;HIS 166;ARG 219 | LYS 39(PLP binding) | |||
| 1xqkA01 |
|
|
|
|
|
LYS 39;HIS 166;ARG 219 | LYS 39(PLP binding) | KCX 129(carbamylated Lys) | ||
| 1xqkB01 |
|
|
|
|
|
LYS 39;HIS 166;ARG 219 | LYS 39(PLP binding) | KCX 129(carbamylated Lys) | ||
| 1xqlA01 |
|
|
|
|
|
LYS 39;HIS 166;ARG 219 | LYS 39(PLP binding) | KCX 129(carbamylated Lys) | ||
| 1xqlB01 |
|
|
|
|
|
LYS 39;HIS 166;ARG 219 | LYS 39(PLP binding) | KCX 129(carbamylated Lys) | ||
| 2sfpA01 |
|
|
|
|
|
LYS 39;HIS 166;ARG 219 | LYS 39(PLP binding) | KCX 129(carbamylated Lys) | ||
| 2sfpB01 |
|
|
|
|
|
LYS 39;HIS 166;ARG 219 | LYS 39(PLP binding) | KCX 129(carbamylated Lys) | ||
| 1rcqA01 |
|
|
|
|
|
LYS 33;HIS 158;ARG 208 | LYS 33(PLP binding) | KCX 122(carbamylated Lys) | ||
| 1vfhA01 |
|
|
|
|
|
LYS 38;HIS 168;ARG 224 | LYS 38(PLP binding) | KCX 129(carbamylated Lys) | ||
| 1vfsA01 |
|
|
|
|
|
LYS 38;HIS 168;ARG 224 | LYS 38(PLP binding) | KCX 129(carbamylated Lys) | ||
| 1vfsB01 |
|
|
|
|
|
LYS 1038;HIS 1168;ARG 1224 | LYS 1038(PLP binding) | KCX 1129(carbamylated Lys) | ||
| 1vftA01 |
|
|
|
|
|
LYS 38;HIS 168;ARG 224 | LYS 38(PLP binding) | KCX 129(carbamylated Lys) | ||
| 1vftB01 |
|
|
|
|
|
LYS 1038;HIS 1168;ARG 1224 | LYS 1038(PLP binding) | KCX 1129(carbamylated Lys) | ||
| 1xfcA01 |
|
|
|
|
|
LYS 42;HIS 172;ARG 228 | LYS 42(PLP binding) | |||
| 1xfcB01 |
|
|
|
|
|
LYS 42;HIS 172;ARG 228 | LYS 42(PLP binding) | |||
| 1bd0A02 |
|
|
|
|
|
TYR 265;ASP 313 | ||||
| 1bd0B02 |
|
|
|
|
|
TYR 265;ASP 313 | ||||
| 1epvA02 |
|
|
|
|
|
TYR 265;ASP 313 | ||||
| 1epvB02 |
|
|
|
|
|
TYR 265;ASP 313 | ||||
| 1ftxA02 |
|
|
|
|
|
TYR 265;ASP 313 | ||||
| 1ftxB02 |
|
|
|
|
|
TYR 265;ASP 313 | ||||
| 1l6fA02 |
|
|
|
|
|
TYR 265;ASP 313 | ||||
| 1l6fB02 |
|
|
|
|
|
TYR 265;ASP 313 | ||||
| 1l6gA02 |
|
|
|
|
|
TYR 265;ASP 313 | ||||
| 1l6gB02 |
|
|
|
|
|
TYR 265;ASP 313 | ||||
| 1niuA02 |
|
|
|
|
|
TYR 265;ASP 313 | ||||
| 1niuB02 |
|
|
|
|
|
TYR 265;ASP 313 | ||||
| 1sftA02 |
|
|
|
|
|
TYR 265;ASP 313 | ||||
| 1sftB02 |
|
|
|
|
|
TYR 265;ASP 313 | ||||
| 1xqkA02 |
|
|
|
|
|
;ASP 313 | mutant Y265F | |||
| 1xqkB02 |
|
|
|
|
|
;ASP 313 | mutant Y265F | |||
| 1xqlA02 |
|
|
|
|
|
;ASP 313 | mutant Y265F | |||
| 1xqlB02 |
|
|
|
|
|
;ASP 313 | mutant Y265F | |||
| 2sfpA02 |
|
|
|
|
|
TYR 265;ASP 313 | ||||
| 2sfpB02 |
|
|
|
|
|
TYR 265;ASP 313 | ||||
| 1rcqA02 |
|
|
|
|
|
TYR 253;ASP 302 | ||||
| 1vfhA02 |
|
|
|
|
|
TYR 270;ASP 319 | ||||
| 1vfsA02 |
|
|
|
|
|
TYR 270;ASP 319 | ||||
| 1vfsB02 |
|
|
|
|
|
TYR 1270;ASP 1319 | ||||
| 1vftA02 |
|
|
|
|
|
TYR 270;ASP 319 | ||||
| 1vftB02 |
|
|
|
|
|
TYR 1270;ASP 1319 | ||||
| 1xfcA02 |
|
|
|
|
|
TYR 271;ASP 320 | ||||
| 1xfcB02 |
|
|
|
|
|
;ASP 320 | invisible 264-278 | |||
| 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] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 7034778 |
| Journal | Biochemistry |
| Year | 1981 |
| Volume | 20 |
| Pages | 7539-46 |
| Authors | Wang EA, Walsh C |
| Title |
Characteristics of beta, |
| Related PDB | |
| Related UniProtKB | |
| [2] | |
| Resource | |
| Comments | |
| Medline ID | |
| 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. |
| Related PDB | |
| Related UniProtKB | |
| [3] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 3730360 |
| Journal | Biochemistry |
| Year | 1986 |
| Volume | 25 |
| Pages | 3275-82 |
| 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. |
| Related PDB | |
| Related UniProtKB | |
| [4] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 3118951 |
| Journal | Biochemistry |
| 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. |
| Related PDB | |
| Related UniProtKB | |
| [5] | |
| Resource | |
| Comments | |
| Medline ID | |
| 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. |
| Related PDB | |
| Related UniProtKB | |
| [6] | |
| Resource | |
| Comments | |
| Medline ID | |
| 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. |
| Related PDB | |
| Related UniProtKB | |
| [7] | |
| Resource | |
| Comments | |
| Medline ID | |
| 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. |
| Related PDB | |
| Related UniProtKB | |
| [8] | |
| Resource | |
| Comments |
X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS), |
| 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] | |
| Resource | |
| 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] | |
| Resource | |
| 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] | |
| Resource | |
| 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 PDB | |
| Related UniProtKB | P10724 |
| [12] | |
| Resource | |
| Comments | |
| Medline ID | |
| 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. |
| Related PDB | |
| Related UniProtKB | |
| [13] | |
| Resource | |
| Comments |
ACTIVE SITES, |
| 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 PDB | |
| Related UniProtKB | P10724 |
| [14] | |
| Resource | |
| Comments | |
| Medline ID | |
| 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. |
| Related PDB | |
| Related UniProtKB | |
| [15] | |
| Resource | |
| Comments | |
| Medline ID | |
| 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. |
| Related PDB | |
| Related UniProtKB | |
| [16] | |
| Resource | |
| Comments | |
| Medline ID | |
| 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. |
| Related PDB | |
| Related UniProtKB | |
| [17] | |
| Resource | |
| Comments | |
| Medline ID | |
| 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. |
| Related PDB | |
| Related UniProtKB | |
| [18] | |
| Resource | |
| Comments | X-ray crystallography |
| Medline ID | |
| 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 |
| Related UniProtKB | |
| [19] | |
| Resource | |
| Comments | X-ray crystallography |
| Medline ID | |
| 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 |
| Related UniProtKB | |
| [20] | |
| Resource | |
| Comments | |
| Medline ID | |
| 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, |
| Related PDB | 1rcq |
| Related UniProtKB | |
| [21] | |
| Resource | |
| Comments | |
| Medline ID | |
| 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. |
| Related PDB | |
| Related UniProtKB | |
| [22] | |
| Resource | |
| Comments | |
| Medline ID | |
| 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. |
| Related PDB | |
| Related UniProtKB | |
| [23] | |
| Resource | |
| Comments | |
| Medline ID | |
| 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. |
| Related PDB | |
| Related UniProtKB | |
| [24] | |
| Resource | |
| Comments | |
| Medline ID | |
| 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. |
| Related PDB | |
| Related UniProtKB | |
| [25] | |
| Resource | |
| Comments | |
| Medline ID | |
| 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 |
| Related UniProtKB | |
| [26] | |
| Resource | |
| Comments | |
| Medline ID | |
| 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. |
| Related PDB | |
| Related UniProtKB | |
| [27] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 15581583 |
| Journal | Arch Biochem Biophys |
| Year | 2005 |
| Volume | 433 |
| Pages | 279-87 |
| Authors | Toney MD |
| Title | Reaction specificity in pyridoxal phosphate enzymes. |
| Related PDB | |
| Related UniProtKB | |
| [28] | |
| Resource | |
| Comments | X-ray crystallography |
| Medline ID | |
| 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 |
| Related UniProtKB | |
| [29] | |
| Resource | |
| Comments | |
| Medline ID | |
| 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 |
| Related UniProtKB | |
| Comments |
|---|
|
This enzyme belongs to the type-III PLP-dependent enzyme superfamily.
This enzyme catalyzes racemization, (A) Formation of an external aldimine (with amine group of L-Ala, (B) Isomerization (change in the position of double-bond), (C) Isomerization (change in the position of double-bond), (D) Formation of internal aldimine, These reactions proceed in the following way: (A) Formation of external aldimine (PLP-L-Ala; I00049) (see [8], (A1) The interaction of Arg219 through His166 with Tyr265' (from the adjacent chain) keeps the sidechain of Tyr265' unprotonated. (A2) Tyr265' acts as a general base to deprotonate and activate the protonated amine group of substrate, (A3) The deprotonated amine group of L-Ala makes a nucleophilic attack on the C4' atom of PLP, (A4) Proton transfer from the amine group of L-Ala to epsilon-nitrogen atom of Lys39 must occur (probably through alpha-carboxyl group, (A5) The lone pair of the amine group of L-Ala makes the second nucleophilic attack on the C4' atom, (B) Isomerization (change in the position of double-bond), (B1) Protonated Tyr265' must be deprotonated, (B2) Tyr265' acts as a general base to deprotonate the alpha-proton of the L-amino acid substrate, (B3) Arg219 interacts with the N1 atom of PLP, (C) Isomerization (change in the position of double-bond), (C1) Arg219 interacts with the N1 atom of PLP, (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). (D) Formation of internal aldimine, (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, (D2) Proton transfer from the epsilon-nitrogen atom of Lys39 to the amine group of D-Ala must occur (probably through alpha-carboxyl group, (D3) The lone pair of the amine nitrogen of Lys39 can attack on the C4' atom to form a double-bond, (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. |
| Created | Updated |
|---|---|
| 2005-04-18 | 2015-07-23 |