DB code: D00105

RLCP classification 6.40.521010.5520 : Double-bonded atom exchange
8.211.591510.5527 : Isomerization
6.10.85210.5901 : Double-bonded atom exchange
6.20.85210.5511 : Double-bonded atom exchange
8.211.591510.5526 : Isomerization
6.30.97710.5300 : Double-bonded atom exchange
CATH domain 3.30.470.10 : D-amino Acid Aminotransferase; Chain A, domain 1 Catalytic domain
3.20.10.10 : D-amino Acid Aminotransferase; Chain A, domain 2 Catalytic domain
E.C. 2.6.1.21
CSA 1daa
M-CSA 1daa
MACiE M0066

CATH domain Related DB codes (homologues)
3.30.470.10 : D-amino Acid Aminotransferase; Chain A, domain 1 D00106
3.20.10.10 : D-amino Acid Aminotransferase; Chain A, domain 2 D00106

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P19938 D-alanine aminotransferase
EC 2.6.1.21
D-amino acid aminotransferase
D-amino acid transaminase
DAAT
D-aspartate aminotransferase
PF01063 (Aminotran_4)
[Graphical View]

KEGG enzyme name
D-amino-acid transaminase
D-aspartate transaminase
D-alanine aminotransferase
D-aspartic aminotransferase
D-alanine-D-glutamate transaminase
D-alanine transaminase
D-amino acid aminotransferase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P19938 DAAA_BACYM D-alanine + 2-oxoglutarate = pyruvate + D- glutamate. Homodimer. Pyridoxal phosphate.

KEGG Pathways
Map code Pathways E.C.
MAP00310 Lysine degradation
MAP00330 Arginine and proline metabolism
MAP00360 Phenylalanine metabolism
MAP00472 D-Arginine and D-ornithine metabolism
MAP00473 D-Alanine metabolism
MAP00550 Peptidoglycan biosynthesis

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00018 C00133 C00026 C00022 C00217 I00029 I00032 I00030 C00647 I00006 I00033 I00031
E.C. (carbinolabine)
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)
Type aromatic ring (with nitrogen atoms),phosphate group/phosphate ion amino acids carbohydrate,carboxyl group carbohydrate,carboxyl group amino acids,carboxyl group
ChEBI 18405
15570
57416
30915
32816
15966
PubChem 1051
71080
7311725
51
1060
23327
1a0gA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1a0gB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1daaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1daaB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1g2wA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:ACT Unbound Unbound Unbound Unbound
1g2wB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:ACT Unbound Unbound Unbound Unbound
2daaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2daaB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2dabA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2dabB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3daaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3daaB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
4daaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
4daaB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
5daaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
5daaB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1a0gA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:PMP Unbound Unbound Unbound Unbound Unbound Unbound Intermediate-bound:PMP
1a0gB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:PMP Unbound Unbound Unbound Unbound Unbound Unbound Intermediate-bound:PMP
1daaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1daaB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1g2wA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1g2wB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2daaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:DCS Unbound Unbound Unbound Unbound Unbound Intermediate-analogue:DCS Unbound
2daaB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:DCS Unbound Unbound Unbound Unbound Unbound Intermediate-analogue:DCS Unbound
2dabA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2dabB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3daaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:PDD Unbound Unbound Unbound Unbound Intermediate-bound:PDD Unbound Unbound
3daaB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:PDD Unbound Unbound Unbound Unbound Intermediate-bound:PDD Unbound Unbound
4daaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound Unbound Unbound
4daaB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound Unbound Unbound
5daaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound Unbound Unbound
5daaB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [8], [16], [19], [21]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1a0gA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 31;HIS 100
1a0gB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 31;HIS 100
1daaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 31;HIS 100
1daaB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 31;HIS 100
1g2wA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 31;HIS 100
1g2wB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 31;HIS 100
2daaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 31;HIS 100
2daaB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 31;HIS 100
2dabA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 31;HIS 100
2dabB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 31;HIS 100
3daaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 31;HIS 100
3daaB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 31;HIS 100
4daaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 31;HIS 100
4daaB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 31;HIS 100
5daaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 31;HIS 100
5daaB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 31;HIS 100
1a0gA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 145;GLU 177 LYS 145(PLP binding) mutant L201A
1a0gB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 145;GLU 177 LYS 145(PLP binding) mutant L201A
1daaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 145;GLU 177 LYS 145(PLP binding)
1daaB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 145;GLU 177 LYS 145(PLP binding)
1g2wA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 145; LYS 145(PLP binding) mutant E177S
1g2wB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ; mutant E177S, invisible 145
2daaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 145;GLU 177 LYS 145(PLP binding)
2daaB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 145;GLU 177 LYS 145(PLP binding)
2dabA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 145;GLU 177 LYS 145(PLP binding) mutant L201A
2dabB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 145;GLU 177 LYS 145(PLP binding) mutant L201A
3daaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 145;GLU 177 LYS 145(PLP binding)
3daaB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 145;GLU 177 LYS 145(PLP binding)
4daaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 145;GLU 177 LYS 145(PLP binding)
4daaB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 145;GLU 177 LYS 145(PLP binding)
5daaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 145; LYS 145(PLP binding) mutant E177K
5daaB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 145; LYS 145(PLP binding) mutant E177K

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[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]
Resource
Comments
Medline ID
PubMed ID 4950474
Journal Adv Enzymol Relat Areas Mol Biol
Year 1971
Volume 35
Pages 79-134
Authors Dunathan HC
Title Stereochemical aspects of pyridoxal phosphate catalysis.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
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
Title Activity and spectroscopic properties of bacterial D-amino acid transaminase after multiple site-directed mutagenesis of a single tryptophan residue.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 2496746
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
Title Site-directed mutagenesis of the cysteinyl residues and the active-site serine residue of bacterial D-amino acid transaminase.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 2914916
Journal J Biol Chem
Year 1989
Volume 264
Pages 2445-9
Authors Tanizawa K, Masu Y, Asano S, Tanaka H, Soda K
Title Thermostable D-amino acid aminotransferase from a thermophilic Bacillus species. Purification, characterization, and active site sequence determination.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 2125047
Journal J Biol Chem
Year 1990
Volume 265
Pages 22306-12
Authors Futaki S, Ueno H, Martinez del Pozo A, Pospischil MA, Manning JM, Ringe D, Stoddard B, Tanizawa K, Yoshimura T, Soda K
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.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 1902115
Journal Biochemistry
Year 1991
Volume 30
Pages 4072-7
Authors Nishimura K, Tanizawa K, Yoshimura T, Esaki N, Futaki S, Manning JM, Soda K
Title Effect of substitution of a lysyl residue that binds pyridoxal phosphate in thermostable D-amino acid aminotransferase by arginine and alanine.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 1445909
Journal Biochemistry
Year 1992
Volume 31
Pages 11748-54
Authors Yoshimura T, Bhatia MB, Manning JM, Ringe D, Soda K
Title Partial reactions of bacterial D-amino acid transaminase with asparagine substituted for the lysine that binds coenzyme pyridoxal 5'-phosphate.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 8463224
Journal J Biol Chem
Year 1993
Volume 268
Pages 6932-8
Authors Bhatia MB, Futaki S, Ueno H, Manning JM, Ringe D, Yoshimura T, Soda K
Title Kinetic and stereochemical comparison of wild-type and active-site K145Q mutant enzyme of bacterial D-amino acid transaminase.
Related PDB
Related UniProtKB
[9]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.94 ANGSTROMS)
Medline ID 95352651
PubMed ID 7626635
Journal Biochemistry
Year 1995
Volume 34
Pages 9661-9
Authors Sugio S, Petsko GA, Manning JM, Soda K, Ringe D
Title Crystal structure of a D-amino acid aminotransferase: how the protein controls stereoselectivity.
Related PDB 1daa
Related UniProtKB P19938
[10]
Resource
Comments
Medline ID
PubMed ID 7592528
Journal J Biochem (Tokyo)
Year 1995
Volume 117
Pages 691-6
Authors Kishimoto K, Yoshimura T, Esaki N, Sugio S, Manning JM, Soda K
Title Role of leucine 201 of thermostable D-amino acid aminotransferase from a thermophile, Bacillus sp. YM-1.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 8580849
Journal Protein Sci
Year 1995
Volume 4
Pages 2578-86
Authors Van Ophem PW, Pospischil MA, Ringe D, Peisach D, Petsko G, Soda K, Manning JM
Title Catalytic ability and stability of two recombinant mutants of D-amino acid transaminase involved in coenzyme binding.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 8652553
Journal Biochemistry
Year 1996
Volume 35
Pages 2112-6
Authors Martinez del Pozo A, van Ophem PW, Ringe D, Petsko G, Soda K, Manning JM
Title Interaction of pyridoxal 5'-phosphate with tryptophan-139 at the subunit interface of dimeric D-amino acid transaminase.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 9063963
Journal Biosci Biotechnol Biochem
Year 1996
Volume 60
Pages 181-7
Authors Yoshimura T, Jhee KH, Soda K
Title Stereospecificity for the hydrogen transfer and molecular evolution of pyridoxal enzymes.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 9498563
Journal J Biochem (Tokyo)
Year 1997
Volume 122
Pages 1182-9
Authors Kishimoto K, Yoshimura T, Soda K, Esaki N
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.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 9163511
Journal J Biochem (Tokyo)
Year 1997
Volume 121
Pages 637-41
Authors Okada K, Hirotsu K, Sato M, Hayashi H, Kagamiyama H
Title Three-dimensional structure of Escherichia coli branched-chain amino acid aminotransferase at 2.5 A resolution.
Related PDB
Related UniProtKB
[16]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS)
Medline ID 98206914
PubMed ID 9538014
Journal Biochemistry
Year 1998
Volume 37
Pages 4958-67
Authors Peisach D, Chipman DM, Van Ophem PW, Manning JM, Ringe D
Title Crystallographic study of steps along the reaction pathway of D-amino acid aminotransferase.
Related PDB 2daa 3daa 4daa
Related UniProtKB P19938
[17]
Resource
Comments
Medline ID
PubMed ID 9914259
Journal Curr Opin Struct Biol
Year 1998
Volume 8
Pages 759-69
Authors Jansonius JN
Title Structure, evolution and action of vitamin B6-dependent enzymes.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 9792912
Journal J Biochem (Tokyo)
Year 1998
Volume 124
Pages 905-10
Authors Fuchikami Y, Yoshimura T, Gutierrez A, Soda K, Esaki N
Title Construction and properties of a fragmentary D-amino acid aminotransferase.
Related PDB
Related UniProtKB
[19]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS)
Medline ID 98420361
PubMed ID 9749913
Journal Protein Eng
Year 1998
Volume 11
Pages 613-9
Authors Sugio S, Kashima A, Kishimoto K, Peisach D, Petsko GA, Ringe D, Yoshimura T, Esaki N
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.
Related PDB 1a0g 2dab
Related UniProtKB P19938
[20]
Resource
Comments
Medline ID
PubMed ID
Journal J Microbiol Biotechnol
Year 1999
Volume 9
Pages 695-703
Authors Jhee KH, Yoshimura T, Kurokawa Y, Esaki N, Soda K
Title A stereochemical aspect of pyridoxal 5 '-phosphate dependent enzyme reactions and molecular evolution.
Related PDB
Related UniProtKB
[21]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 9930994
Journal Biochemistry
Year 1999
Volume 38
Pages 1323-31
Authors van Ophem PW, Peisach D, Erickson SD, Soda K, Ringe D, Manning JM
Title Effects of the E177K mutation in D-amino acid transaminase. Studies on an essential coenzyme anchoring group that contributes to stereochemical fidelity.
Related PDB 5daa
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 10800595
Journal Adv Enzymol Relat Areas Mol Biol
Year 2000
Volume 74
Pages 129-84
Authors Mehta PK, Christen P
Title The molecular evolution of pyridoxal-5'-phosphate-dependent enzymes.
Related PDB
Related UniProtKB
[23]
Resource
Comments
Medline ID
PubMed ID 10630999
Journal Biochemistry
Year 2000
Volume 39
Pages 381-7
Authors Kishimoto K, Yasuda C, Manning JM
Title Reversible dissociation/association of D-amino acid transaminase subunits: properties of isolated active dimers and inactive monomers.
Related PDB
Related UniProtKB
[24]
Resource
Comments
Medline ID
PubMed ID 11106434
Journal Eur J Biochem
Year 2000
Volume 267
Pages 7218-23
Authors Gutierrez A, Yoshimura T, Fuchikami Y, Esaki N
Title Modulation of activity and substrate specificity by modifying the backbone length of the distant interdomain loop of D-amino acid aminotransferase.
Related PDB
Related UniProtKB
[25]
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
[26]
Resource
Comments
Medline ID
PubMed ID 11933244
Journal Chem Rec
Year 2001
Volume 1
Pages 373-84
Authors Soda K, Yoshimura T, Esaki N
Title Stereospecificity for the hydrogen transfer of pyridoxal enzyme reactions.
Related PDB
Related UniProtKB
[27]
Resource
Comments
Medline ID
PubMed ID 11642362
Journal Prog Nucleic Acid Res Mol Biol
Year 2001
Volume 70
Pages 175-206
Authors Hutson S
Title Structure and function of branched chain aminotransferases.
Related PDB
Related UniProtKB
[28]
Resource
Comments
Medline ID
PubMed ID 12297014
Journal J Biochem Mol Biol
Year 2002
Volume 35
Pages 306-12
Authors Ro HS
Title Effects of salts on the conformation and catalytic properties of d-amino acid aminotransferase.
Related PDB
Related UniProtKB

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.

Created Updated
2004-03-18 2009-02-26