DB code: D00255

CATH domain 3.90.1150.10 : Aspartate Aminotransferase, domain 1
3.40.640.10 : Aspartate Aminotransferase; domain 2 Catalytic domain
E.C. 4.1.1.64
CSA 1d7r
M-CSA 1d7r
MACiE

CATH domain Related DB codes (homologues)
3.40.640.10 : Aspartate Aminotransferase; domain 2 D00085 D00092 D00101 D00102 D00103 D00104 D00107 D00108 D00109 D00257 D00258 D00265 D00269 D00515 M00031 D00279
3.90.1150.10 : Aspartate Aminotransferase, domain 1 D00085 D00092 D00101 D00102 D00103 D00104 D00107 D00108 D00109 D00257 D00258 D00265 D00269 D00515 M00031 D00279

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P16932 2,2-dialkylglycine decarboxylase
DGD
EC 4.1.1.64
PF00202 (Aminotran_3)
[Graphical View]

KEGG enzyme name
2,2-dialkylglycine decarboxylase (pyruvate)
dialkyl amino acid (pyruvate) decarboxylase
alpha-dialkyl amino acid transaminase
2,2-dialkyl-2-amino acid-pyruvate aminotransferase
L-alanine-alpha-ketobutyrate aminotransferase
dialkylamino-acid decarboxylase (pyruvate)
2,2-dialkylglycine carboxy-lyase (amino-transferring)

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P16932 DGDA_BURCE 2,2-dialkylglycine + pyruvate = dialkyl ketone + CO(2) + L-alanine. Homotetramer. Pyridoxal phosphate.

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00018 C00238 C02623 C00022 C02146 C00011 C00041
E.C.
Compound Pyridoxal phosphate Potassium 2,2-Dialkylglycine Pyruvate Dialkyl ketone CO2 L-Alanine
Type aromatic ring (with nitrogen atoms),phosphate group/phosphate ion univalent metal (Na+, K+) amino acids carbohydrate,carboxyl group carbohydrate others amino acids
ChEBI 18405
29103
32816
16526
16977
57972
PubChem 1051
813
1060
280
5950
7311724
1d7rA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1d7sA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1d7uA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1d7vA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1dgdA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1dgeA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1dkaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2dkbA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1m0nA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1m0oA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1m0pA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1m0qA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1d7rA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:5PA Bound:__K Unbound Unbound Unbound Unbound Unbound Intermediate-bound:5PA
1d7sA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:DCS Bound:__K Unbound Unbound Unbound Unbound Unbound Intermediate-analogue:DCS
1d7uA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:LCS Bound:__K Unbound Unbound Unbound Unbound Unbound Intermediate-analogue:LCS
1d7vA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:NMA Bound:__K Unbound Unbound Unbound Unbound Unbound Intermediate-bound:NMA
1dgdA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Analogue:_LI Unbound Unbound Unbound Unbound Unbound Unbound
1dgeA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Analogue:_RB Unbound Unbound Unbound Unbound Unbound Unbound
1dkaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:LYS_272 Bound:__K Unbound Unbound Unbound Unbound Unbound Unbound
2dkbA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:LYS_272 Analogue:_NA Unbound Unbound Unbound Unbound Unbound Unbound
1m0nA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:HCP Bound:__K Unbound Unbound Unbound Unbound Unbound Intermediate-analogue:HCP
1m0oA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:MPM Bound:__K Unbound Unbound Unbound Unbound Unbound Intermediate-analogue:MPM
1m0pA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:ELP Bound:__K Unbound Unbound Unbound Unbound Unbound Intermediate-analogue:ELP
1m0qA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:EPC Bound:__K Unbound Unbound Unbound Unbound Unbound Intermediate-analogue:EPC

Reference for Active-site residues
resource references E.C.
literature [6]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1d7rA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLN 52
1d7sA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLN 52
1d7uA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLN 52
1d7vA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLN 52
1dgdA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLN 52 mutant Q15H
1dgeA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLN 52 mutant Q15H
1dkaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLN 52
2dkbA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLN 52
1m0nA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLN 52
1m0oA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLN 52
1m0pA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLN 52
1m0qA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLN 52
1d7rA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 272 LEU 78;SER 80;THR 303;VAL 305;ASP 307 LYS 272(PLP binding)
1d7sA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 272 LEU 78;SER 80;THR 303;VAL 305;ASP 307 LYS 272(PLP binding)
1d7uA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 272 LEU 78;SER 80;THR 303;VAL 305;ASP 307 LYS 272(PLP binding)
1d7vA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 272 LEU 78;SER 80;THR 303;VAL 305;ASP 307 LYS 272(PLP binding)
1dgdA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 272 LEU 78;SER 80;THR 303;VAL 305;ASP 307 LYS 272(PLP binding)
1dgeA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 272 LEU 78;SER 80;THR 303;VAL 305;ASP 307 LYS 272(PLP binding)
1dkaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 272 LEU 78;SER 80;THR 303;VAL 305;ASP 307 LYS 272(PLP binding)
2dkbA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 272 LEU 78;SER 80;THR 303;VAL 305;ASP 307 LYS 272(PLP binding)
1m0nA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 272 LEU 78;SER 80;THR 303;VAL 305;ASP 307 LYS 272(PLP binding)
1m0oA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 272 LEU 78;SER 80;THR 303;VAL 305;ASP 307 LYS 272(PLP binding)
1m0pA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 272 LEU 78;SER 80;THR 303;VAL 305;ASP 307 LYS 272(PLP binding)
1m0qA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 272 LEU 78;SER 80;THR 303;VAL 305;ASP 307 LYS 272(PLP binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[3]
p.757
[6]
Figure 21, p.169-171
[8]
Scheme 1, p.315-319
[9]
p.1382-1383
[11]
Scheme 1, Fig.8

References
[1]
Resource
Comments
Medline ID
PubMed ID 1722256
Journal J Mol Biol
Year 1991
Volume 222
Pages 873-5
Authors Toney MD, Keller JW, Pauptit RA, Jaeger J, Wise MK, Sauder U, Jansonius JN
Title Crystallization and preliminary X-ray diffraction studies of dialkylglycine decarboxylase, a decarboxylating transaminase.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 8405393
Journal FEBS Lett
Year 1993
Volume 331
Pages 145-9
Authors Pascarella S, Schirch V, Bossa F
Title Similarity between serine hydroxymethyltransferase and other pyridoxal phosphate-dependent enzymes.
Related PDB
Related UniProtKB
[3]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
Medline ID 93342511
PubMed ID 8342040
Journal Science
Year 1993
Volume 261
Pages 756-9
Authors Toney MD, Hohenester E, Cowan SW, Jansonius JN
Title Dialkylglycine decarboxylase structure: bifunctional active site and alkali metal sites.
Related PDB 1dka 2dkb
Related UniProtKB P16932
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS), AND REVISIONS TO 51; 81-82 AND 307-311.
Medline ID 95034792
PubMed ID 7947767
Journal Biochemistry
Year 1994
Volume 33
Pages 13561-70
Authors Hohenester E, Keller JW, Jansonius JN
Title An alkali metal ion size-dependent switch in the active site structure of dialkylglycine decarboxylase.
Related PDB 1dgd 1dge
Related UniProtKB P16932
[5]
Resource
Comments
Medline ID
PubMed ID 8003988
Journal Protein Sci
Year 1994
Volume 3
Pages 701-5
Authors Pascarella S, Bossa F
Title Similarity between pyridoxal/pyridoxamine phosphate-dependent enzymes involved in dideoxy and deoxyaminosugar biosynthesis and other pyridoxal phosphate enzymes.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
Medline ID 95097385
PubMed ID 7799433
Journal J Mol Biol
Year 1995
Volume 245
Pages 151-79
Authors Toney MD, Hohenester E, Keller JW, Jansonius JN
Title Structural and mechanistic analysis of two refined crystal structures of the pyridoxal phosphate-dependent enzyme dialkylglycine decarboxylase.
Related PDB
Related UniProtKB P16932
[7]
Resource
Comments
Medline ID
PubMed ID 9548963
Journal Biochemistry
Year 1998
Volume 37
Pages 5761-9
Authors Zhou X, Kay S, Toney MD
Title Coexisting kinetically distinguishable forms of dialkylglycine decarboxylase engendered by alkali metal ions.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 9890912
Journal Biochemistry
Year 1999
Volume 38
Pages 311-20
Authors Zhou X, Toney MD
Title pH studies on the mechanism of the pyridoxal phosphate-dependent dialkylglycine decarboxylase.
Related PDB
Related UniProtKB
[9]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID 20027099
PubMed ID 10556038
Journal J Mol Biol
Year 1999
Volume 294
Pages 193-200
Authors Malashkevich VN, Strop P, Keller JW, Jansonius JN, Toney MD
Title Crystal structures of dialkylglycine decarboxylase inhibitor complexes.
Related PDB 1d7r 1d7s 1d7u 1d7v
Related UniProtKB P16932
[10]
Resource
Comments
Medline ID
PubMed ID 11170465
Journal Biochemistry
Year 2001
Volume 40
Pages 1378-84
Authors Toney MD
Title Computational studies on nonenzymatic and enzymatic pyridoxal phosphate catalyzed decarboxylations of 2-aminoisobutyrate.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 11170464
Journal Biochemistry
Year 2001
Volume 40
Pages 1367-77
Authors Zhou X, Jin X, Medhekar R, Chen X, Dieckmann T, Toney MD
Title Rapid kinetic and isotopic studies on dialkylglycine decarboxylase.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 12369820
Journal Biochemistry
Year 2002
Volume 41
Pages 12320-8
Authors Liu W, Rogers CJ, Fisher AJ, Toney MD
Title Aminophosphonate inhibitors of dialkylglycine decarboxylase: structural basis for slow binding inhibition.
Related PDB 1m0n 1m0o 1m0p 1m0q
Related UniProtKB

Comments
This enzyme belongs to the class-III PLP-dependent aminotransferase family.
According to the literature [4] & [6], potassium ion (K+) is an activating factor, whilst sodium ion (Na+) and lithium ion (Li+) are inhibitory at site 1 (sidechain of Ser80 & Asp307; mainchain of Leu78, Thr303 & Val305), which is located close to the PLP phosphate group at the dimer interface. These ions play a role as a switch for the active site, although they are not directly involved in catalysis.
According to the literature [8], [10], [11] & [12], this enzyme catalyzes Decarboxylation and Transamination.
These reactions are composed of several basic reactions:
The decarboxylation consists of the following reactions;
(A1) Formation of external aldimine (with dialkylglycine),
(A2) Elimination of carboxylate group,
(A3) Schiff-base deforming,
The transamination consists of the following reactions;
(B1) New Schiff-base forming (with pyruvate),
(B2) Isomerization,
(B3) Formation of internal aldimine (or deformation of external aldimine).

Created Updated
2004-06-29 2009-02-26