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
16977
57972
15570
57416
PubChem 1051
5950
7311724
71080
7311725
1bd0A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:IN5 Unbound Unbound Intermediate-analogue:IN5 Unbound Unbound
1bd0B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:IN5 Unbound Unbound Intermediate-analogue:IN5 Unbound Unbound
1epvA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:DCS Unbound Unbound Unbound Intermediate-analogue:DCS Unbound
1epvB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:DCS Unbound Unbound Unbound Intermediate-analogue:DCS Unbound
1ftxA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:EPC Unbound Unbound Unbound Unbound Intermediate-analogue:EPC
1ftxB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:EPC Unbound Unbound Unbound Unbound Intermediate-analogue:EPC
1l6fA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:PP3 Unbound Unbound Intermediate-bound:PP3 Unbound Unbound
1l6fB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:PP3 Unbound Unbound Intermediate-bound:PP3 Unbound Unbound
1l6gA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:PDD Unbound Unbound Unbound Unbound Intermediate-bound:PDD
1l6gB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:PDD Unbound Unbound Unbound Unbound Intermediate-bound:PDD
1niuA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:DCS Unbound Unbound Unbound Intermediate-analogue:DCS Unbound
1niuB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:DCS Unbound Unbound Unbound Intermediate-analogue:DCS Unbound
1sftA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound
1sftB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound
1xqkA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:PMH Unbound Unbound Unbound Intermediate-analogue:PMH Unbound
1xqkB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:PMH Unbound Unbound Unbound Intermediate-analogue:PMH Unbound
1xqlA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:PLP-PMH-PMP Unbound Unbound Unbound Intermediate-analogue:PMH Intermediate-analogue:PMP-4AX
1xqlB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:PLP-PMH-PMP Unbound Unbound Unbound Intermediate-analogue:PMH Intermediate-analogue:PMP-4AX
2sfpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound
2sfpB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound
1rcqA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound
1vfhA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound
1vfsA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:DCS Unbound Unbound Unbound Intermediate-analogue:DCS Unbound
1vfsB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:DCS Unbound Unbound Unbound Intermediate-analogue:DCS Unbound
1vftA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:DCS Unbound Unbound Unbound Intermediate-analogue:DCS Unbound
1vftB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:DCS Unbound Unbound Unbound Intermediate-analogue:DCS Unbound
1xfcA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound
1xfcB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound
1bd0A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1bd0B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1epvA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1epvB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1ftxA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1ftxB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1l6fA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1l6fB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1l6gA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1l6gB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1niuA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1niuB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1sftA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:ACT Unbound Unbound Unbound Unbound
1sftB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:ACT Unbound Unbound Unbound Unbound
1xqkA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1xqkB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1xqlA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:ACY Unbound Unbound Unbound Unbound
1xqlB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:ACY Unbound Unbound Unbound Unbound
2sfpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:PPI Unbound Unbound Unbound Unbound
2sfpB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:PPI Unbound Unbound Unbound Unbound
1rcqA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:DLY Unbound Unbound Unbound
1vfhA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1vfsA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1vfsB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1vftA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1vftB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1xfcA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1xfcB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 39;HIS 166;ARG 219 LYS 39(PLP binding)
1bd0B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 39;HIS 166;ARG 219 LYS 39(PLP binding)
1epvA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 39;HIS 166;ARG 219 LYS 39(PLP binding) KCX 129(carbamylated Lys)
1epvB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 39;HIS 166;ARG 219 LYS 39(PLP binding) KCX 129(carbamylated Lys)
1ftxA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 39;HIS 166;ARG 219 LYS 39(PLP binding) KCX 129(carbamylated Lys)
1ftxB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 39;HIS 166;ARG 219 LYS 39(PLP binding) KCX 129(carbamylated Lys)
1l6fA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 39;HIS 166;ARG 219 LYS 39(PLP binding) KCX 129(carbamylated Lys)
1l6fB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 39;HIS 166;ARG 219 LYS 39(PLP binding) KCX 129(carbamylated Lys)
1l6gA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 39;HIS 166;ARG 219 LYS 39(PLP binding) KCX 129(carbamylated Lys)
1l6gB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 39;HIS 166;ARG 219 LYS 39(PLP binding) KCX 129(carbamylated Lys)
1niuA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 39;HIS 166;ARG 219 LYS 39(PLP binding) KCX 129(carbamylated Lys)
1niuB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 39;HIS 166;ARG 219 LYS 39(PLP binding) KCX 129(carbamylated Lys)
1sftA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 39;HIS 166;ARG 219 LYS 39(PLP binding)
1sftB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 39;HIS 166;ARG 219 LYS 39(PLP binding)
1xqkA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 39;HIS 166;ARG 219 LYS 39(PLP binding) KCX 129(carbamylated Lys)
1xqkB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 39;HIS 166;ARG 219 LYS 39(PLP binding) KCX 129(carbamylated Lys)
1xqlA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 39;HIS 166;ARG 219 LYS 39(PLP binding) KCX 129(carbamylated Lys)
1xqlB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 39;HIS 166;ARG 219 LYS 39(PLP binding) KCX 129(carbamylated Lys)
2sfpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 39;HIS 166;ARG 219 LYS 39(PLP binding) KCX 129(carbamylated Lys)
2sfpB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 39;HIS 166;ARG 219 LYS 39(PLP binding) KCX 129(carbamylated Lys)
1rcqA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 33;HIS 158;ARG 208 LYS 33(PLP binding) KCX 122(carbamylated Lys)
1vfhA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 38;HIS 168;ARG 224 LYS 38(PLP binding) KCX 129(carbamylated Lys)
1vfsA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 38;HIS 168;ARG 224 LYS 38(PLP binding) KCX 129(carbamylated Lys)
1vfsB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 1038;HIS 1168;ARG 1224 LYS 1038(PLP binding) KCX 1129(carbamylated Lys)
1vftA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 38;HIS 168;ARG 224 LYS 38(PLP binding) KCX 129(carbamylated Lys)
1vftB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 1038;HIS 1168;ARG 1224 LYS 1038(PLP binding) KCX 1129(carbamylated Lys)
1xfcA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 42;HIS 172;ARG 228 LYS 42(PLP binding)
1xfcB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 42;HIS 172;ARG 228 LYS 42(PLP binding)
1bd0A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 265;ASP 313
1bd0B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 265;ASP 313
1epvA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 265;ASP 313
1epvB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 265;ASP 313
1ftxA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 265;ASP 313
1ftxB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 265;ASP 313
1l6fA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 265;ASP 313
1l6fB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 265;ASP 313
1l6gA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 265;ASP 313
1l6gB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 265;ASP 313
1niuA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 265;ASP 313
1niuB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 265;ASP 313
1sftA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 265;ASP 313
1sftB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 265;ASP 313
1xqkA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASP 313 mutant Y265F
1xqkB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASP 313 mutant Y265F
1xqlA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASP 313 mutant Y265F
1xqlB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASP 313 mutant Y265F
2sfpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 265;ASP 313
2sfpB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 265;ASP 313
1rcqA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 253;ASP 302
1vfhA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 270;ASP 319
1vfsA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 270;ASP 319
1vfsB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 1270;ASP 1319
1vftA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 270;ASP 319
1vftB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 1270;ASP 1319
1xfcA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 271;ASP 320
1xfcB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;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, beta-difluoroalanine and beta, beta, beta -trifluoroalanine as suicide substrates for Escherichia coli B alanine racemase.
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. subtilis.
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. Overproduction, crystallization, and preliminary characterization.
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), 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]
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, 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 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. Chemical rescue studies of Lys39 --> Ala mutant.
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, Pseudomonas aeruginosa, contains both internal and external aldimine forms.
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, 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.)

Created Updated
2005-04-18 2015-07-23