EzCatDB: D00255

DB codeD00255
CATH domainDomain 13.90.1150.10
Domain 23.40.640.10Catalytic domain
E.C.4.1.1.64
CSA1d7r

CATH domainRelated DB codes (homologues)
3.40.640.10D00085,D00092,D00101,D00102,D00103,D00104,D00107,D00108,D00109,D00257,D00258,D00265,D00269,D00515,M00031,D00279
3.90.1150.10D00085,D00092,D00101,D00102,D00103,D00104,D00107,D00108,D00109,D00257,D00258,D00265,D00269,D00515,M00031,D00279

Enzyme Name
Swiss-protKEGG

P16932
Protein name2,2-dialkylglycine decarboxylase2,2-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)
SynonymsDGD
EC 4.1.1.64


Swiss-prot:Accession NumberP16932
Entry nameDGDA_BURCE
Activity2,2-dialkylglycine + pyruvate = dialkyl ketone + CO(2) + L-alanine.
SubunitHomotetramer.
Subcellular location
CofactorPyridoxal phosphate.


CofactorsSubstratesProductsintermediates
KEGG-idC00018C00238C02623C00022C02146C00011C00041
CompoundPyridoxal phosphatePotassium2,2-DialkylglycinePyruvateDialkyl ketoneCO2L-Alanine
Typearomatic ring (with nitrogen atoms),phosphate group/phosphate ionunivalent metal (Na+, K+)amino acidscarbohydrate,carboxyl groupcarbohydrateothersamino acids
1d7rA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1d7sA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1d7uA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1d7vA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1dgdA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1dgeA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1dkaA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2dkbA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1m0nA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1m0oA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1m0pA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1m0qA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1d7rA02Analogue:5PABound:__KUnboundUnboundUnboundUnboundUnboundIntermediate-bound:5PA
1d7sA02Analogue:DCSBound:__KUnboundUnboundUnboundUnboundUnboundIntermediate-analogue:DCS
1d7uA02Analogue:LCSBound:__KUnboundUnboundUnboundUnboundUnboundIntermediate-analogue:LCS
1d7vA02Analogue:NMABound:__KUnboundUnboundUnboundUnboundUnboundIntermediate-bound:NMA
1dgdA02Bound:PLPAnalogue:_LIUnboundUnboundUnboundUnboundUnboundUnbound
1dgeA02Bound:PLPAnalogue:_RBUnboundUnboundUnboundUnboundUnboundUnbound
1dkaA02Bound:LYS 272Bound:__KUnboundUnboundUnboundUnboundUnboundUnbound
2dkbA02Bound:LYS 272Analogue:_NAUnboundUnboundUnboundUnboundUnboundUnbound
1m0nA02Analogue:HCPBound:__KUnboundUnboundUnboundUnboundUnboundIntermediate-analogue:HCP
1m0oA02Analogue:MPMBound:__KUnboundUnboundUnboundUnboundUnboundIntermediate-analogue:MPM
1m0pA02Analogue:ELPBound:__KUnboundUnboundUnboundUnboundUnboundIntermediate-analogue:ELP
1m0qA02Analogue:EPCBound:__KUnboundUnboundUnboundUnboundUnboundIntermediate-analogue:EPC

Active-site residues
resource
literature [6]
pdbCatalytic residuesCofactor-binding residuesModified residuescomment
1d7rA01GLN 52



1d7sA01GLN 52



1d7uA01GLN 52



1d7vA01GLN 52



1dgdA01GLN 52


mutant Q15H
1dgeA01GLN 52


mutant Q15H
1dkaA01GLN 52



2dkbA01GLN 52



1m0nA01GLN 52



1m0oA01GLN 52



1m0pA01GLN 52



1m0qA01GLN 52



1d7rA02LYS 272
LEU 78;SER 80;THR 303;VAL 305;ASP 307
LYS 272(PLP binding)

1d7sA02LYS 272
LEU 78;SER 80;THR 303;VAL 305;ASP 307
LYS 272(PLP binding)

1d7uA02LYS 272
LEU 78;SER 80;THR 303;VAL 305;ASP 307
LYS 272(PLP binding)

1d7vA02LYS 272
LEU 78;SER 80;THR 303;VAL 305;ASP 307
LYS 272(PLP binding)

1dgdA02LYS 272
LEU 78;SER 80;THR 303;VAL 305;ASP 307
LYS 272(PLP binding)

1dgeA02LYS 272
LEU 78;SER 80;THR 303;VAL 305;ASP 307
LYS 272(PLP binding)

1dkaA02LYS 272
LEU 78;SER 80;THR 303;VAL 305;ASP 307
LYS 272(PLP binding)

2dkbA02LYS 272
LEU 78;SER 80;THR 303;VAL 305;ASP 307
LYS 272(PLP binding)

1m0nA02LYS 272
LEU 78;SER 80;THR 303;VAL 305;ASP 307
LYS 272(PLP binding)

1m0oA02LYS 272
LEU 78;SER 80;THR 303;VAL 305;ASP 307
LYS 272(PLP binding)

1m0pA02LYS 272
LEU 78;SER 80;THR 303;VAL 305;ASP 307
LYS 272(PLP binding)

1m0qA02LYS 272
LEU 78;SER 80;THR 303;VAL 305;ASP 307
LYS 272(PLP binding)


References for Catalytic Mechanism
ReferencesSectionsNo. 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]
PubMed ID1722256
JournalJ Mol Biol
Year1991
Volume222
Pages873-5
AuthorsToney MD, Keller JW, Pauptit RA, Jaeger J, Wise MK, Sauder U, Jansonius JN
TitleCrystallization and preliminary X-ray diffraction studies of dialkylglycine decarboxylase, a decarboxylating transaminase.
[2]
PubMed ID8405393
JournalFEBS Lett
Year1993
Volume331
Pages145-9
AuthorsPascarella S, Schirch V, Bossa F
TitleSimilarity between serine hydroxymethyltransferase and other pyridoxal phosphate-dependent enzymes.
[3]
CommentsX-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
Medline ID93342511
PubMed ID8342040
JournalScience
Year1993
Volume261
Pages756-9
AuthorsToney MD, Hohenester E, Cowan SW, Jansonius JN
TitleDialkylglycine decarboxylase structure: bifunctional active site and alkali metal sites.
Related PDB1dka,2dkb
Related Swiss-protP16932
[4]
CommentsX-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS), AND REVISIONS TO 51; 81-82 AND 307-311.
Medline ID95034792
PubMed ID7947767
JournalBiochemistry
Year1994
Volume33
Pages13561-70
AuthorsHohenester E, Keller JW, Jansonius JN
TitleAn alkali metal ion size-dependent switch in the active site structure of dialkylglycine decarboxylase.
Related PDB1dgd,1dge
Related Swiss-protP16932
[5]
PubMed ID8003988
JournalProtein Sci
Year1994
Volume3
Pages701-5
AuthorsPascarella S, Bossa F
TitleSimilarity between pyridoxal/pyridoxamine phosphate-dependent enzymes involved in dideoxy and deoxyaminosugar biosynthesis and other pyridoxal phosphate enzymes.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
Medline ID95097385
PubMed ID7799433
JournalJ Mol Biol
Year1995
Volume245
Pages151-79
AuthorsToney MD, Hohenester E, Keller JW, Jansonius JN
TitleStructural and mechanistic analysis of two refined crystal structures of the pyridoxal phosphate-dependent enzyme dialkylglycine decarboxylase.
Related Swiss-protP16932
[7]
PubMed ID9548963
JournalBiochemistry
Year1998
Volume37
Pages5761-9
AuthorsZhou X, Kay S, Toney MD
TitleCoexisting kinetically distinguishable forms of dialkylglycine decarboxylase engendered by alkali metal ions.
[8]
PubMed ID9890912
JournalBiochemistry
Year1999
Volume38
Pages311-20
AuthorsZhou X, Toney MD
TitlepH studies on the mechanism of the pyridoxal phosphate-dependent dialkylglycine decarboxylase.
[9]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID20027099
PubMed ID10556038
JournalJ Mol Biol
Year1999
Volume294
Pages193-200
AuthorsMalashkevich VN, Strop P, Keller JW, Jansonius JN, Toney MD
TitleCrystal structures of dialkylglycine decarboxylase inhibitor complexes.
Related PDB1d7r,1d7s,1d7u,1d7v
Related Swiss-protP16932
[10]
PubMed ID11170465
JournalBiochemistry
Year2001
Volume40
Pages1378-84
AuthorsToney MD
TitleComputational studies on nonenzymatic and enzymatic pyridoxal phosphate catalyzed decarboxylations of 2-aminoisobutyrate.
[11]
PubMed ID11170464
JournalBiochemistry
Year2001
Volume40
Pages1367-77
AuthorsZhou X, Jin X, Medhekar R, Chen X, Dieckmann T, Toney MD
TitleRapid kinetic and isotopic studies on dialkylglycine decarboxylase.
[12]
PubMed ID12369820
JournalBiochemistry
Year2002
Volume41
Pages12320-8
AuthorsLiu W, Rogers CJ, Fisher AJ, Toney MD
TitleAminophosphonate inhibitors of dialkylglycine decarboxylase: structural basis for slow binding inhibition.
Related PDB1m0n,1m0o,1m0p,1m0q

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).

createdupdated
2004-06-292009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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