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
 18405
 		29103
 29103
 		32816
 32816
 		16526
 16526
 		16977
 57972
 16977
 57972
PubChem 1051
 1051
 		813
 813
 		1060
 1060
 		280
 280
 		5950
 7311724
 5950
 7311724
1d7rA01 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1d7sA01 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1d7uA01 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1d7vA01 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1dgdA01 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1dgeA01 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1dkaA01 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2dkbA01 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1m0nA01 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1m0oA01 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1m0pA01 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1m0qA01 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1d7rA02 Analogue:5PA Bound:__K Unbound Unbound Unbound Unbound Unbound Intermediate-bound:5PA
1d7sA02 Analogue:DCS Bound:__K Unbound Unbound Unbound Unbound Unbound Intermediate-analogue:DCS
1d7uA02 Analogue:LCS Bound:__K Unbound Unbound Unbound Unbound Unbound Intermediate-analogue:LCS
1d7vA02 Analogue:NMA Bound:__K Unbound Unbound Unbound Unbound Unbound Intermediate-bound:NMA
1dgdA02 Bound:PLP Analogue:_LI Unbound Unbound Unbound Unbound Unbound Unbound
1dgeA02 Bound:PLP Analogue:_RB Unbound Unbound Unbound Unbound Unbound Unbound
1dkaA02 Bound:LYS_272 Bound:__K Unbound Unbound Unbound Unbound Unbound Unbound
2dkbA02 Bound:LYS_272 Analogue:_NA Unbound Unbound Unbound Unbound Unbound Unbound
1m0nA02 Analogue:HCP Bound:__K Unbound Unbound Unbound Unbound Unbound Intermediate-analogue:HCP
1m0oA02 Analogue:MPM Bound:__K Unbound Unbound Unbound Unbound Unbound Intermediate-analogue:MPM
1m0pA02 Analogue:ELP Bound:__K Unbound Unbound Unbound Unbound Unbound Intermediate-analogue:ELP
1m0qA02 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 GLN 52
1d7sA01 GLN 52
1d7uA01 GLN 52
1d7vA01 GLN 52
1dgdA01 GLN 52 mutant Q15H
1dgeA01 GLN 52 mutant Q15H
1dkaA01 GLN 52
2dkbA01 GLN 52
1m0nA01 GLN 52
1m0oA01 GLN 52
1m0pA01 GLN 52
1m0qA01 GLN 52
1d7rA02 LYS 272 LEU 78;SER 80;THR 303;VAL 305;ASP 307 LYS 272(PLP binding)
1d7sA02 LYS 272 LEU 78;SER 80;THR 303;VAL 305;ASP 307 LYS 272(PLP binding)
1d7uA02 LYS 272 LEU 78;SER 80;THR 303;VAL 305;ASP 307 LYS 272(PLP binding)
1d7vA02 LYS 272 LEU 78;SER 80;THR 303;VAL 305;ASP 307 LYS 272(PLP binding)
1dgdA02 LYS 272 LEU 78;SER 80;THR 303;VAL 305;ASP 307 LYS 272(PLP binding)
1dgeA02 LYS 272 LEU 78;SER 80;THR 303;VAL 305;ASP 307 LYS 272(PLP binding)
1dkaA02 LYS 272 LEU 78;SER 80;THR 303;VAL 305;ASP 307 LYS 272(PLP binding)
2dkbA02 LYS 272 LEU 78;SER 80;THR 303;VAL 305;ASP 307 LYS 272(PLP binding)
1m0nA02 LYS 272 LEU 78;SER 80;THR 303;VAL 305;ASP 307 LYS 272(PLP binding)
1m0oA02 LYS 272 LEU 78;SER 80;THR 303;VAL 305;ASP 307 LYS 272(PLP binding)
1m0pA02 LYS 272 LEU 78;SER 80;THR 303;VAL 305;ASP 307 LYS 272(PLP binding)
1m0qA02 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