DGDA_BURCE
ID DGDA_BURCE Reviewed; 433 AA.
AC P16932;
DT 01-AUG-1990, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 25-MAY-2022, entry version 123.
DE RecName: Full=2,2-dialkylglycine decarboxylase;
DE Short=DGD;
DE EC=4.1.1.64;
GN Name=dgdA;
OS Burkholderia cepacia (Pseudomonas cepacia).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Burkholderiaceae; Burkholderia; Burkholderia cepacia complex.
OX NCBI_TaxID=292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 2-20 AND
RP 261-276.
RX PubMed=2180928; DOI=10.1016/s0021-9258(19)39393-7;
RA Keller J.W., Baurick K.B., Rutt G.C., O'Malley M.V., Sonafrank N.L.,
RA Reynolds R.A., Ebbesson L.O.E., Vajdos F.F.;
RT "Pseudomonas cepacia 2,2-dialkylglycine decarboxylase. Sequence and
RT expression in Escherichia coli of structural and repressor genes.";
RL J. Biol. Chem. 265:5531-5539(1990).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
RX PubMed=8342040; DOI=10.1126/science.8342040;
RA Toney M.D., Hohenester E., Cowan S.W., Jansonius J.N.;
RT "Dialkylglycine decarboxylase structure: bifunctional active site and
RT alkali metal sites.";
RL Science 261:756-759(1993).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS), AND SEQUENCE REVISION TO 52; 82-83
RP AND 308-312.
RX PubMed=7947767; DOI=10.1021/bi00250a008;
RA Hohenester E., Keller J.W., Jansonius J.N.;
RT "An alkali metal ion size-dependent switch in the active site structure of
RT dialkylglycine decarboxylase.";
RL Biochemistry 33:13561-13570(1994).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
RX PubMed=7799433; DOI=10.1006/jmbi.1994.0014;
RA Toney M.D., Hohenester E., Keller J.W., Jansonius J.N.;
RT "Structural and mechanistic analysis of two refined crystal structures of
RT the pyridoxal phosphate-dependent enzyme dialkylglycine decarboxylase.";
RL J. Mol. Biol. 245:151-179(1995).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
RX PubMed=10556038; DOI=10.1006/jmbi.1999.3254;
RA Malashkevich V.N., Strop P., Keller J.W., Jansonius J.N., Toney M.D.;
RT "Crystal structures of dialkylglycine decarboxylase inhibitor complexes.";
RL J. Mol. Biol. 294:193-200(1999).
CC -!- FUNCTION: The dialkylglycine decarboxylase is of interest because it
CC normally catalyzes both decarboxylation and amino transfer. It may be
CC more properly described as a decarboxylating aminotransferase rather
CC than an aminotransferring decarboxylase.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2,2-dialkylglycine + H(+) + pyruvate = CO2 + dialkyl ketone +
CC L-alanine; Xref=Rhea:RHEA:16073, ChEBI:CHEBI:15361,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:18044,
CC ChEBI:CHEBI:57689, ChEBI:CHEBI:57972; EC=4.1.1.64;
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC -!- SUBUNIT: Homotetramer.
CC -!- MISCELLANEOUS: The enzyme may have evolved to use the rare
CC dialkylglycines of cosmic origin, or it may be part of a metabolic
CC pathway for breaking down cytotoxic peptides and the constituent amino
CC acids.
CC -!- SIMILARITY: Belongs to the class-III pyridoxal-phosphate-dependent
CC aminotransferase family. {ECO:0000305}.
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DR EMBL; J05282; AAA50844.1; -; Genomic_DNA.
DR PIR; A35173; A35173.
DR PDB; 1D7R; X-ray; 2.00 A; A=1-433.
DR PDB; 1D7S; X-ray; 2.05 A; A=1-433.
DR PDB; 1D7U; X-ray; 1.95 A; A=1-433.
DR PDB; 1D7V; X-ray; 2.80 A; A=1-433.
DR PDB; 1DGD; X-ray; 2.80 A; A=2-433.
DR PDB; 1DGE; X-ray; 2.80 A; A=2-433.
DR PDB; 1DKA; X-ray; 2.60 A; A=1-433.
DR PDB; 1M0N; X-ray; 2.20 A; A=1-433.
DR PDB; 1M0O; X-ray; 2.40 A; A=1-433.
DR PDB; 1M0P; X-ray; 2.60 A; A=1-433.
DR PDB; 1M0Q; X-ray; 2.00 A; A=1-433.
DR PDB; 1Z3Z; X-ray; 2.90 A; A=3-433.
DR PDB; 1ZC9; X-ray; 2.00 A; A=1-433.
DR PDB; 1ZOB; X-ray; 2.75 A; A=1-433.
DR PDB; 1ZOD; X-ray; 1.80 A; A=1-433.
DR PDB; 2DKB; X-ray; 2.10 A; A=1-433.
DR PDBsum; 1D7R; -.
DR PDBsum; 1D7S; -.
DR PDBsum; 1D7U; -.
DR PDBsum; 1D7V; -.
DR PDBsum; 1DGD; -.
DR PDBsum; 1DGE; -.
DR PDBsum; 1DKA; -.
DR PDBsum; 1M0N; -.
DR PDBsum; 1M0O; -.
DR PDBsum; 1M0P; -.
DR PDBsum; 1M0Q; -.
DR PDBsum; 1Z3Z; -.
DR PDBsum; 1ZC9; -.
DR PDBsum; 1ZOB; -.
DR PDBsum; 1ZOD; -.
DR PDBsum; 2DKB; -.
DR AlphaFoldDB; P16932; -.
DR SMR; P16932; -.
DR STRING; 292.DM42_5757; -.
DR DrugBank; DB03787; (5-Hydroxy-6-methyl-4-{[(E)-(3-oxo-1,2-oxazolidin-4-ylidene)amino]methyl}-3-pyridinyl)methyl dihydrogen phosphate.
DR DrugBank; DB02038; D-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-N,O-cycloserylamide.
DR DrugBank; DB02849; N-Pyridoxyl-1-Amino-Cyclopropanecarboxylic Acid-5-Monophosphate.
DR DrugBank; DB04241; N-Pyridoxyl-2-Methylalanine-5-Phosphate.
DR PRIDE; P16932; -.
DR KEGG; ag:AAA50844; -.
DR eggNOG; COG0160; Bacteria.
DR BRENDA; 4.1.1.64; 1028.
DR SABIO-RK; P16932; -.
DR EvolutionaryTrace; P16932; -.
DR GO; GO:0047432; F:2,2-dialkylglycine decarboxylase (pyruvate) activity; IEA:UniProtKB-EC.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:InterPro.
DR GO; GO:0008483; F:transaminase activity; IEA:InterPro.
DR CDD; cd00610; OAT_like; 1.
DR Gene3D; 3.40.640.10; -; 1.
DR Gene3D; 3.90.1150.10; -; 1.
DR InterPro; IPR005814; Aminotrans_3.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR Pfam; PF00202; Aminotran_3; 1.
DR PIRSF; PIRSF000521; Transaminase_4ab_Lys_Orn; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
DR PROSITE; PS00600; AA_TRANSFER_CLASS_3; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Decarboxylase; Direct protein sequencing; Lyase;
KW Pyridoxal phosphate.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:2180928"
FT CHAIN 2..433
FT /note="2,2-dialkylglycine decarboxylase"
FT /id="PRO_0000120509"
FT MOD_RES 272
FT /note="N6-(pyridoxal phosphate)lysine"
FT HELIX 7..16
FT /evidence="ECO:0007829|PDB:1ZOD"
FT STRAND 31..34
FT /evidence="ECO:0007829|PDB:1ZOD"
FT STRAND 36..38
FT /evidence="ECO:0007829|PDB:1ZOD"
FT STRAND 44..47
FT /evidence="ECO:0007829|PDB:1ZOD"
FT HELIX 50..53
FT /evidence="ECO:0007829|PDB:1ZOD"
FT HELIX 62..74
FT /evidence="ECO:0007829|PDB:1ZOD"
FT HELIX 85..97
FT /evidence="ECO:0007829|PDB:1ZOD"
FT STRAND 104..109
FT /evidence="ECO:0007829|PDB:1ZOD"
FT HELIX 111..126
FT /evidence="ECO:0007829|PDB:1ZOD"
FT STRAND 130..134
FT /evidence="ECO:0007829|PDB:1ZOD"
FT HELIX 143..147
FT /evidence="ECO:0007829|PDB:1ZOD"
FT STRAND 151..153
FT /evidence="ECO:0007829|PDB:1ZOB"
FT STRAND 155..157
FT /evidence="ECO:0007829|PDB:1ZOD"
FT STRAND 164..167
FT /evidence="ECO:0007829|PDB:1ZOD"
FT STRAND 172..174
FT /evidence="ECO:0007829|PDB:1D7U"
FT STRAND 178..183
FT /evidence="ECO:0007829|PDB:1D7U"
FT HELIX 185..199
FT /evidence="ECO:0007829|PDB:1ZOD"
FT STRAND 204..209
FT /evidence="ECO:0007829|PDB:1ZOD"
FT STRAND 211..213
FT /evidence="ECO:0007829|PDB:1ZOD"
FT TURN 214..217
FT /evidence="ECO:0007829|PDB:1ZOD"
FT STRAND 218..220
FT /evidence="ECO:0007829|PDB:1D7U"
FT HELIX 225..235
FT /evidence="ECO:0007829|PDB:1ZOD"
FT STRAND 239..243
FT /evidence="ECO:0007829|PDB:1ZOD"
FT TURN 245..252
FT /evidence="ECO:0007829|PDB:1ZOD"
FT STRAND 253..256
FT /evidence="ECO:0007829|PDB:1ZOD"
FT HELIX 258..261
FT /evidence="ECO:0007829|PDB:1ZOD"
FT STRAND 266..270
FT /evidence="ECO:0007829|PDB:1ZOD"
FT HELIX 272..275
FT /evidence="ECO:0007829|PDB:1ZOD"
FT STRAND 281..285
FT /evidence="ECO:0007829|PDB:1ZOD"
FT HELIX 287..295
FT /evidence="ECO:0007829|PDB:1ZOD"
FT TURN 303..306
FT /evidence="ECO:0007829|PDB:1ZOD"
FT HELIX 308..323
FT /evidence="ECO:0007829|PDB:1ZOD"
FT HELIX 326..347
FT /evidence="ECO:0007829|PDB:1ZOD"
FT STRAND 351..357
FT /evidence="ECO:0007829|PDB:1ZOD"
FT STRAND 360..368
FT /evidence="ECO:0007829|PDB:1ZOD"
FT TURN 369..372
FT /evidence="ECO:0007829|PDB:1ZOD"
FT HELIX 378..388
FT /evidence="ECO:0007829|PDB:1ZOD"
FT STRAND 395..397
FT /evidence="ECO:0007829|PDB:1M0O"
FT STRAND 404..407
FT /evidence="ECO:0007829|PDB:1ZOD"
FT HELIX 415..432
FT /evidence="ECO:0007829|PDB:1ZOD"
SQ SEQUENCE 433 AA; 46444 MW; EF441EC8DF8C37FE CRC64;
MSLNDDATFW RNARQHLVRY GGTFEPMIIE RAKGSFVYDA DGRAILDFTS GQMSAVLGHC
HPEIVSVIGE YAGKLDHLFS GMLSRPVVDL ATRLANITPP GLDRALLLST GAESNEAAIR
MAKLVTGKYE IVGFAQSWHG MTGAAASATY SAGRKGVGPA AVGSFAIPAP FTYRPRFERN
GAYDYLAELD YAFDLIDRQS SGNLAAFIAE PILSSGGIIE LPDGYMAALK RKCEARGMLL
ILDEAQTGVG RTGTMFACQR DGVTPDILTL SKTLGAGLPL AAIVTSAAIE ERAHELGYLF
YTTHVSDPLP AAVGLRVLDV VQRDGLVARA NVMGDRLRRG LLDLMERFDC IGDVRGRGLL
LGVEIVKDRR TKEPADGLGA KITRECMNLG LSMNIVQLPG MGGVFRIAPP LTVSEDEIDL
GLSLLGQAIE RAL
