F
IPR000183

Ornithine/DAP/Arg decarboxylase

InterPro entry
Short nameOrn/DAP/Arg_de-COase
Overlapping
homologous
superfamilies
 
PLP-binding barrel (IPR029066)
family relationships

Description

Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities
[2, 1]
. Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. PLP-dependent decarboxylases exhibit two different structural folds, Fold I and Fold III. This family belong to the Fold III group which proceed with retention of configuration at the site of decarboxylation, with the exception of diaminopimelate decarboxylase (DAPDC) and D-ornithine/D-lysine decarboxylase (DOKDC) from Salmonella enterica serovar typhimurium, that are known as stereoinverting decarboxylases
[5]
. The proteins contain a conserved lysine residue which is known, in mouse ODC
[3]
, to be the site of attachment of the pyridoxal-phosphate group and it is thought to be responsible for protonation of the product, thus resulting in the retention of configuration for decarboxylation of l-amino acids and inversion for decarboxylation of d-amino acids
[5]
. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate-binding region
[4]
.

These enzymes are collectively known as group IV decarboxylases, and include ornithine and arginine decarboxylases, and diaminopimelate decarboxylase (DAP)
[1]
.

References

1.Multiple evolutionary origin of pyridoxal-5'-phosphate-dependent amino acid decarboxylases. Sandmeier E, Hale TI, Christen P. Eur. J. Biochem. 221, 997-1002, (1994). View articlePMID: 8181483

2.Pseudomonas aeruginosa diaminopimelate decarboxylase: evolutionary relationship with other amino acid decarboxylases. Martin C, Cami B, Yeh P, Stragier P, Parsot C, Patte JC. Mol. Biol. Evol. 5, 549-59, (1988). View articlePMID: 3143046

3.Mechanism of the irreversible inactivation of mouse ornithine decarboxylase by alpha-difluoromethylornithine. Characterization of sequences at the inhibitor and coenzyme binding sites. Poulin R, Lu L, Ackermann B, Bey P, Pegg AE. J. Biol. Chem. 267, 150-8, (1992). View articlePMID: 1730582

4.Nucleotide sequence and analysis of the speA gene encoding biosynthetic arginine decarboxylase in Escherichia coli. Moore RC, Boyle SM. J. Bacteriol. 172, 4631-40, (1990). View articlePMID: 2198270

5.Crystal Structure of d-Ornithine/d-Lysine Decarboxylase, a Stereoinverting Decarboxylase: Implications for Substrate Specificity and Stereospecificity of Fold III Decarboxylases. Phillips RS, Poteh P, Krajcovic D, Miller KA, Hoover TR. Biochemistry 58, 1038-1042, (2019). PMID: 30699288

GO terms

biological process

  • None

cellular component

  • None

Cross References

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