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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

ConSurf analysis of amino acid conservation shows possible interacting surfaces on PanD and PanM. a Structure of E. coli pro-PanD tetramer. Residues that are more conserved in Class I (PanM-dependent) than in Class II (PanM-independent) gammaproteobacterial PanD homologs are highlighted in red. b Structure of E. coli PanM monomer bound to CoASH with conserved residues highlighted in red.
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Fig4: ConSurf analysis of amino acid conservation shows possible interacting surfaces on PanD and PanM. a Structure of E. coli pro-PanD tetramer. Residues that are more conserved in Class I (PanM-dependent) than in Class II (PanM-independent) gammaproteobacterial PanD homologs are highlighted in red. b Structure of E. coli PanM monomer bound to CoASH with conserved residues highlighted in red.

Mentions: It is known that l-aspartate-α-decarboxylases and PanM interact [10], but the interaction domain has not been identified. We posited that the domain of PanM responsible for interaction with l-aspartate-α-decarboxylase might contain conserved amino acids responsible for the interaction. Given the above data, it followed that l-aspartate-α-decarboxylase residues interacting with PanM should be conserved in the class of homologues requiring PanM for activation (Class I), but not conserved in the class of homologues that did not require PanM (Class II). The ConSurf server [13] was used to calculate evolutionary conservation of amino acids in PanM, and Class I and Class II l-aspartate-α-decarboxylase homologues. Since Class I enzymes were only found in Gammaproteobacteria, we limited our conservation analysis of Class II l-aspartate-α-decarboxylases to the Gammaproteobacteria. Residues that were more conserved in Class I than Class II l-aspartate-α-decarboxylases were highlighted on the crystal structure of E. colil-aspartate-α-decarboxylase zymogen (PDB 1PPY) [14] (Fig. 4a). Residues conserved in all PanM homologues were highlighted on the nuclear magnetic resonance (NMR) solution structure of E. coli YhhK (Cort, J. R., Yee, A., Arrowsmith, C. H. and Kennedy, M. A.; unpublished; PDB 2K5T) (Fig. 4b); the E. coli YhhK is now known as PanZ [15].Fig. 4


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)

ConSurf analysis of amino acid conservation shows possible interacting surfaces on PanD and PanM. a Structure of E. coli pro-PanD tetramer. Residues that are more conserved in Class I (PanM-dependent) than in Class II (PanM-independent) gammaproteobacterial PanD homologs are highlighted in red. b Structure of E. coli PanM monomer bound to CoASH with conserved residues highlighted in red.
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig4: ConSurf analysis of amino acid conservation shows possible interacting surfaces on PanD and PanM. a Structure of E. coli pro-PanD tetramer. Residues that are more conserved in Class I (PanM-dependent) than in Class II (PanM-independent) gammaproteobacterial PanD homologs are highlighted in red. b Structure of E. coli PanM monomer bound to CoASH with conserved residues highlighted in red.
Mentions: It is known that l-aspartate-α-decarboxylases and PanM interact [10], but the interaction domain has not been identified. We posited that the domain of PanM responsible for interaction with l-aspartate-α-decarboxylase might contain conserved amino acids responsible for the interaction. Given the above data, it followed that l-aspartate-α-decarboxylase residues interacting with PanM should be conserved in the class of homologues requiring PanM for activation (Class I), but not conserved in the class of homologues that did not require PanM (Class II). The ConSurf server [13] was used to calculate evolutionary conservation of amino acids in PanM, and Class I and Class II l-aspartate-α-decarboxylase homologues. Since Class I enzymes were only found in Gammaproteobacteria, we limited our conservation analysis of Class II l-aspartate-α-decarboxylases to the Gammaproteobacteria. Residues that were more conserved in Class I than Class II l-aspartate-α-decarboxylases were highlighted on the crystal structure of E. colil-aspartate-α-decarboxylase zymogen (PDB 1PPY) [14] (Fig. 4a). Residues conserved in all PanM homologues were highlighted on the nuclear magnetic resonance (NMR) solution structure of E. coli YhhK (Cort, J. R., Yee, A., Arrowsmith, C. H. and Kennedy, M. A.; unpublished; PDB 2K5T) (Fig. 4b); the E. coli YhhK is now known as PanZ [15].Fig. 4

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