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Protein

2,2-dialkylglycine decarboxylase

Gene

dgdA

Organism
Burkholderia cepacia (Pseudomonas cepacia)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

The dialkylglycine decarboxylase is of interest because it normally catalyzes both decarboxylation and amino transfer. It may be more properly described as a decarboxylating aminotransferase rather than an aminotransferring decarboxylase.

Catalytic activityi

2,2-dialkylglycine + pyruvate = dialkyl ketone + CO2 + L-alanine.

Cofactori

GO - Molecular functioni

  1. 2,2-dialkylglycine decarboxylase (pyruvate) activity Source: UniProtKB-EC
  2. pyridoxal phosphate binding Source: InterPro
  3. transaminase activity Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

BRENDAi4.1.1.64. 1028.
SABIO-RKP16932.

Names & Taxonomyi

Protein namesi
Recommended name:
2,2-dialkylglycine decarboxylase (EC:4.1.1.64)
Short name:
DGD
Gene namesi
Name:dgdA
OrganismiBurkholderia cepacia (Pseudomonas cepacia)
Taxonomic identifieri292 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeBurkholderiaBurkholderia cepacia complex

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 4334322,2-dialkylglycine decarboxylasePRO_0000120509Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei272 – 2721N6-(pyridoxal phosphate)lysine

Interactioni

Subunit structurei

Homotetramer.

Structurei

Secondary structure

1
433
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi7 – 1610Combined sources
Beta strandi31 – 344Combined sources
Beta strandi36 – 383Combined sources
Beta strandi44 – 474Combined sources
Helixi50 – 534Combined sources
Helixi62 – 7413Combined sources
Helixi85 – 9713Combined sources
Beta strandi104 – 1096Combined sources
Helixi111 – 12616Combined sources
Beta strandi130 – 1345Combined sources
Helixi143 – 1475Combined sources
Beta strandi151 – 1533Combined sources
Beta strandi155 – 1573Combined sources
Beta strandi164 – 1674Combined sources
Beta strandi172 – 1743Combined sources
Beta strandi178 – 1836Combined sources
Helixi185 – 19915Combined sources
Beta strandi204 – 2096Combined sources
Beta strandi211 – 2133Combined sources
Turni214 – 2174Combined sources
Beta strandi218 – 2203Combined sources
Helixi225 – 23511Combined sources
Beta strandi239 – 2435Combined sources
Turni245 – 2528Combined sources
Beta strandi253 – 2564Combined sources
Helixi258 – 2614Combined sources
Beta strandi266 – 2705Combined sources
Helixi272 – 2754Combined sources
Beta strandi281 – 2855Combined sources
Helixi287 – 2959Combined sources
Turni303 – 3064Combined sources
Helixi308 – 32316Combined sources
Helixi326 – 34722Combined sources
Beta strandi351 – 3577Combined sources
Beta strandi360 – 3689Combined sources
Turni369 – 3724Combined sources
Helixi378 – 38811Combined sources
Beta strandi395 – 3973Combined sources
Beta strandi404 – 4074Combined sources
Helixi415 – 43218Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1D7RX-ray2.00A1-433[»]
1D7SX-ray2.05A1-433[»]
1D7UX-ray1.95A1-433[»]
1D7VX-ray2.80A1-433[»]
1DGDX-ray2.80A2-433[»]
1DGEX-ray2.80A2-433[»]
1DKAX-ray2.60A1-433[»]
1M0NX-ray2.20A1-433[»]
1M0OX-ray2.40A1-433[»]
1M0PX-ray2.60A1-433[»]
1M0QX-ray2.00A1-433[»]
1Z3ZX-ray2.90A3-433[»]
1ZC9X-ray2.00A1-433[»]
1ZOBX-ray2.75A1-433[»]
1ZODX-ray1.80A1-433[»]
2DKBX-ray2.10A1-433[»]
ProteinModelPortaliP16932.
SMRiP16932. Positions 3-433.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP16932.

Family & Domainsi

Sequence similaritiesi

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
InterProiIPR005814. Aminotrans_3.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]
PANTHERiPTHR11986. PTHR11986. 1 hit.
PfamiPF00202. Aminotran_3. 1 hit.
[Graphical view]
SUPFAMiSSF53383. SSF53383. 1 hit.
PROSITEiPS00600. AA_TRANSFER_CLASS_3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P16932-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSLNDDATFW RNARQHLVRY GGTFEPMIIE RAKGSFVYDA DGRAILDFTS
60 70 80 90 100
GQMSAVLGHC HPEIVSVIGE YAGKLDHLFS GMLSRPVVDL ATRLANITPP
110 120 130 140 150
GLDRALLLST GAESNEAAIR MAKLVTGKYE IVGFAQSWHG MTGAAASATY
160 170 180 190 200
SAGRKGVGPA AVGSFAIPAP FTYRPRFERN GAYDYLAELD YAFDLIDRQS
210 220 230 240 250
SGNLAAFIAE PILSSGGIIE LPDGYMAALK RKCEARGMLL ILDEAQTGVG
260 270 280 290 300
RTGTMFACQR DGVTPDILTL SKTLGAGLPL AAIVTSAAIE ERAHELGYLF
310 320 330 340 350
YTTHVSDPLP AAVGLRVLDV VQRDGLVARA NVMGDRLRRG LLDLMERFDC
360 370 380 390 400
IGDVRGRGLL LGVEIVKDRR TKEPADGLGA KITRECMNLG LSMNIVQLPG
410 420 430
MGGVFRIAPP LTVSEDEIDL GLSLLGQAIE RAL
Length:433
Mass (Da):46,444
Last modified:January 23, 2007 - v3
Checksum:iEF441EC8DF8C37FE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J05282 Genomic DNA. Translation: AAA50844.1.
PIRiA35173.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J05282 Genomic DNA. Translation: AAA50844.1.
PIRiA35173.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1D7RX-ray2.00A1-433[»]
1D7SX-ray2.05A1-433[»]
1D7UX-ray1.95A1-433[»]
1D7VX-ray2.80A1-433[»]
1DGDX-ray2.80A2-433[»]
1DGEX-ray2.80A2-433[»]
1DKAX-ray2.60A1-433[»]
1M0NX-ray2.20A1-433[»]
1M0OX-ray2.40A1-433[»]
1M0PX-ray2.60A1-433[»]
1M0QX-ray2.00A1-433[»]
1Z3ZX-ray2.90A3-433[»]
1ZC9X-ray2.00A1-433[»]
1ZOBX-ray2.75A1-433[»]
1ZODX-ray1.80A1-433[»]
2DKBX-ray2.10A1-433[»]
ProteinModelPortaliP16932.
SMRiP16932. Positions 3-433.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

BRENDAi4.1.1.64. 1028.
SABIO-RKP16932.

Miscellaneous databases

EvolutionaryTraceiP16932.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
InterProiIPR005814. Aminotrans_3.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]
PANTHERiPTHR11986. PTHR11986. 1 hit.
PfamiPF00202. Aminotran_3. 1 hit.
[Graphical view]
SUPFAMiSSF53383. SSF53383. 1 hit.
PROSITEiPS00600. AA_TRANSFER_CLASS_3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Pseudomonas cepacia 2,2-dialkylglycine decarboxylase. Sequence and expression in Escherichia coli of structural and repressor genes."
    Keller J.W., Baurick K.B., Rutt G.C., O'Malley M.V., Sonafrank N.L., Reynolds R.A., Ebbesson L.O.E., Vajdos F.F.
    J. Biol. Chem. 265:5531-5539(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-20 AND 261-276.
  2. "Dialkylglycine decarboxylase structure: bifunctional active site and alkali metal sites."
    Toney M.D., Hohenester E., Cowan S.W., Jansonius J.N.
    Science 261:756-759(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
  3. "An alkali metal ion size-dependent switch in the active site structure of dialkylglycine decarboxylase."
    Hohenester E., Keller J.W., Jansonius J.N.
    Biochemistry 33:13561-13570(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS), SEQUENCE REVISION TO 52; 82-83 AND 308-312.
  4. "Structural and mechanistic analysis of two refined crystal structures of the pyridoxal phosphate-dependent enzyme dialkylglycine decarboxylase."
    Toney M.D., Hohenester E., Keller J.W., Jansonius J.N.
    J. Mol. Biol. 245:151-179(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
  5. "Crystal structures of dialkylglycine decarboxylase inhibitor complexes."
    Malashkevich V.N., Strop P., Keller J.W., Jansonius J.N., Toney M.D.
    J. Mol. Biol. 294:193-200(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).

Entry informationi

Entry nameiDGDA_BURCE
AccessioniPrimary (citable) accession number: P16932
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: January 23, 2007
Last modified: April 1, 2015
This is version 96 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The enzyme may have evolved to use the rare dialkylglycines of cosmic origin, or it may be part of a metabolic pathway for breaking down cytotoxic peptides and the constituent amino acids.

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.