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Phylogenetic and amino acid conservation analyses of bacterial L-aspartate-α-decarboxylase and of its zymogen-maturation protein reveal a putative interaction domain.

Stuecker TN, Bramhacharya S, Hodge-Hanson KM, Suen G, Escalante-Semerena JC - BMC Res Notes (2015)

Bottom Line: This class is found exclusively in the Gammaproteobacteria.Class II L-aspartate-α-decarboxylase zymogens self cleave efficiently in the absence of PanM, and are found in a wide number of bacterial phyla.Phylogenetic and amino acid conservation analyses of PanM revealed a conserved region of PanM distinct from conserved regions found in related Gcn5-related acetyltransferase enzymes (Pfam00583).

View Article: PubMed Central - PubMed

Affiliation: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA. BramhacharyaS@my.hiram.edu.

ABSTRACT

Background: All organisms must synthesize the enzymatic cofactor coenzyme A (CoA) from the precursor pantothenate. Most bacteria can synthesize pantothenate de novo by the condensation of pantoate and β-alanine. The synthesis of β-alanine is catalyzed by L-aspartate-α-decarboxylase (PanD), a pyruvoyl enzyme that is initially synthesized as a zymogen (pro-PanD). Active PanD is generated by self-cleavage of pro-PanD at Gly24-Ser25 creating the active-site pyruvoyl moiety. In Salmonella enterica, this cleavage requires PanM, an acetyl-CoA sensor related to the Gcn5-like N-acetyltransferases. PanM does not acetylate pro-PanD, but the recent publication of the three-dimensional crystal structure of the PanM homologue PanZ in complex with the PanD zymogen of Escherichia coli provides validation to our predictions and provides a framework in which to further examine the cleavage mechanism. In contrast, PanD from bacteria lacking PanM efficiently cleaved in the absence of PanM in vivo.

Results: Using phylogenetic analyses combined with in vivo phenotypic investigations, we showed that two classes of bacterial L-aspartate-α-decarboxylases exist. This classification is based on their posttranslational activation by self-cleavage of its zymogen. Class I L-aspartate-α-decarboxylase zymogens require the acetyl-CoA sensor PanM to be cleaved into active PanD. This class is found exclusively in the Gammaproteobacteria. Class II L-aspartate-α-decarboxylase zymogens self cleave efficiently in the absence of PanM, and are found in a wide number of bacterial phyla. Several members of the Euryarchaeota and Crenarchaeota also contain Class II L-aspartate-α-decarboxylases. Phylogenetic and amino acid conservation analyses of PanM revealed a conserved region of PanM distinct from conserved regions found in related Gcn5-related acetyltransferase enzymes (Pfam00583). This conserved region represents a putative domain for interactions with L-aspartate-α-decarboxylase zymogens. This work may inform future biochemical and structural studies of pro-PanD-PanM interactions.

Conclusions: Experimental results indicate that S. enterica and C. glutamicum L-aspartate-α-decarboxylases represent two different classes of homologues of these enzymes. Class I homologues require PanM for activation, while Class II self cleave in the absence of PanM. Computer modeling of conserved amino acids using structure coordinates of PanM and L-aspartate-α-decarboxylase available in the protein data bank (RCSB PDB) revealed a putative site of interactions, which may help generate models to help understand the molecular details of the self-cleavage mechanism of L-aspartate-α-decarboxylases.

No MeSH data available.


Related in: MedlinePlus

Comparison of PanD protein sequences with residues more conserved in bacteria that synthesize PanM than in bacteria that do not synthesize PanM. Highlighted residues represent potential PanM binding regions. The PanD sequences are shown for five representative bacteria that synthesize PanM (bold), and five representative species that do not (regular text). Residues that are not conserved are shown in yellow font.
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Fig5: Comparison of PanD protein sequences with residues more conserved in bacteria that synthesize PanM than in bacteria that do not synthesize PanM. Highlighted residues represent potential PanM binding regions. The PanD sequences are shown for five representative bacteria that synthesize PanM (bold), and five representative species that do not (regular text). Residues that are not conserved are shown in yellow font.

Mentions: Several conserved regions were present in l-aspartate-α-decarboxylase (Figs. 4a, 5), so further in vitro and in vivo analyses are necessary to determine which conserved region interacts with PanM. However, only one conserved region was observed for PanM (Fig. 4b). Notably, this region was in a unique location when compared to other Gcn5-like N-acetyltransferases (GNATs), the family of proteins to which PanM belongs. In GNATs, the protein substrate binds the acetyltransferase in the same cleft to which acetyl-CoA binds [16]. This allows both substrates to be positioned for transfer of the acetyl moiety from acetyl-CoA to the protein substrate. In PanM, the conserved region was located adjacent to the acetyl-CoA binding cleft rather than in the cleft itself (Figs. 4b, 6). If the conserved region of PanM were the PanD interaction domain, PanD would not be positioned for acetyltransfer, supporting previous studies classifying PanM as an acetyl-CoA sensor [11].Fig. 5


Phylogenetic and amino acid conservation analyses of bacterial L-aspartate-α-decarboxylase and of its zymogen-maturation protein reveal a putative interaction domain.

Stuecker TN, Bramhacharya S, Hodge-Hanson KM, Suen G, Escalante-Semerena JC - BMC Res Notes (2015)

Comparison of PanD protein sequences with residues more conserved in bacteria that synthesize PanM than in bacteria that do not synthesize PanM. Highlighted residues represent potential PanM binding regions. The PanD sequences are shown for five representative bacteria that synthesize PanM (bold), and five representative species that do not (regular text). Residues that are not conserved are shown in yellow font.
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4537548&req=5

Fig5: Comparison of PanD protein sequences with residues more conserved in bacteria that synthesize PanM than in bacteria that do not synthesize PanM. Highlighted residues represent potential PanM binding regions. The PanD sequences are shown for five representative bacteria that synthesize PanM (bold), and five representative species that do not (regular text). Residues that are not conserved are shown in yellow font.
Mentions: Several conserved regions were present in l-aspartate-α-decarboxylase (Figs. 4a, 5), so further in vitro and in vivo analyses are necessary to determine which conserved region interacts with PanM. However, only one conserved region was observed for PanM (Fig. 4b). Notably, this region was in a unique location when compared to other Gcn5-like N-acetyltransferases (GNATs), the family of proteins to which PanM belongs. In GNATs, the protein substrate binds the acetyltransferase in the same cleft to which acetyl-CoA binds [16]. This allows both substrates to be positioned for transfer of the acetyl moiety from acetyl-CoA to the protein substrate. In PanM, the conserved region was located adjacent to the acetyl-CoA binding cleft rather than in the cleft itself (Figs. 4b, 6). If the conserved region of PanM were the PanD interaction domain, PanD would not be positioned for acetyltransfer, supporting previous studies classifying PanM as an acetyl-CoA sensor [11].Fig. 5

Bottom Line: This class is found exclusively in the Gammaproteobacteria.Class II L-aspartate-α-decarboxylase zymogens self cleave efficiently in the absence of PanM, and are found in a wide number of bacterial phyla.Phylogenetic and amino acid conservation analyses of PanM revealed a conserved region of PanM distinct from conserved regions found in related Gcn5-related acetyltransferase enzymes (Pfam00583).

View Article: PubMed Central - PubMed

Affiliation: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA. BramhacharyaS@my.hiram.edu.

ABSTRACT

Background: All organisms must synthesize the enzymatic cofactor coenzyme A (CoA) from the precursor pantothenate. Most bacteria can synthesize pantothenate de novo by the condensation of pantoate and β-alanine. The synthesis of β-alanine is catalyzed by L-aspartate-α-decarboxylase (PanD), a pyruvoyl enzyme that is initially synthesized as a zymogen (pro-PanD). Active PanD is generated by self-cleavage of pro-PanD at Gly24-Ser25 creating the active-site pyruvoyl moiety. In Salmonella enterica, this cleavage requires PanM, an acetyl-CoA sensor related to the Gcn5-like N-acetyltransferases. PanM does not acetylate pro-PanD, but the recent publication of the three-dimensional crystal structure of the PanM homologue PanZ in complex with the PanD zymogen of Escherichia coli provides validation to our predictions and provides a framework in which to further examine the cleavage mechanism. In contrast, PanD from bacteria lacking PanM efficiently cleaved in the absence of PanM in vivo.

Results: Using phylogenetic analyses combined with in vivo phenotypic investigations, we showed that two classes of bacterial L-aspartate-α-decarboxylases exist. This classification is based on their posttranslational activation by self-cleavage of its zymogen. Class I L-aspartate-α-decarboxylase zymogens require the acetyl-CoA sensor PanM to be cleaved into active PanD. This class is found exclusively in the Gammaproteobacteria. Class II L-aspartate-α-decarboxylase zymogens self cleave efficiently in the absence of PanM, and are found in a wide number of bacterial phyla. Several members of the Euryarchaeota and Crenarchaeota also contain Class II L-aspartate-α-decarboxylases. Phylogenetic and amino acid conservation analyses of PanM revealed a conserved region of PanM distinct from conserved regions found in related Gcn5-related acetyltransferase enzymes (Pfam00583). This conserved region represents a putative domain for interactions with L-aspartate-α-decarboxylase zymogens. This work may inform future biochemical and structural studies of pro-PanD-PanM interactions.

Conclusions: Experimental results indicate that S. enterica and C. glutamicum L-aspartate-α-decarboxylases represent two different classes of homologues of these enzymes. Class I homologues require PanM for activation, while Class II self cleave in the absence of PanM. Computer modeling of conserved amino acids using structure coordinates of PanM and L-aspartate-α-decarboxylase available in the protein data bank (RCSB PDB) revealed a putative site of interactions, which may help generate models to help understand the molecular details of the self-cleavage mechanism of L-aspartate-α-decarboxylases.

No MeSH data available.


Related in: MedlinePlus