A Bioinformatics Analysis Reveals a Group of MocR Bacterial Transcriptional Regulators Linked to a Family of Genes Coding for Membrane Proteins

Table 3

SDPs found in the AAT domain of YczR and comparison with the residues occurring in the MocR/other. Putative functions are attributed to homology modelling.

YczR	MocR/other	Putative structural function
Ala9	Gly; large hydrophobic	At the active site mouth
Tyr63	Hydrophobic	Exposed to the solvent
Asp/Glu181	Mostly Ala, Leu, Asn, Thr	Buried; possibly interacting with Arg154
Val213	Glu	Buried; at C-side of Asp214 interacting with pyridine nitrogen of PLP
Glu215	Asp	Buried; possibly interacting with Arg154; next to the Asp214 interacting with pyridine nitrogen of PLP
Gly394	Ala, Gly	In a loop
Arg491	Val, Arg	Points to the active site; at about 7 Å distance from the phenolic oxygen of cofactor; with Ala9, forms part of the active site mouth
Pro493	Asn, Gly, Ser	At the C-terminal end of the β-sheet containing Arg491
Pro70	Mainly polar residues	Exposed in a loop on the opposite side of active site
Thr71	Polar and apolar residues; indels	In a loop; possible interaction with Arg 216
Trp151	Pro, hydrophobic residues	Interface between -helices and inner β-sheet of the major domain
Thr217	Hydrophobic or aromatic	Stacking with the cofactor pyridine ring
Trp296	Polar and apolar residues; in a few cases, Trp also	In the loop containing the aldimine-forming lysine
Arg216	Mainly hydrophobic	Exposed; possible interaction with Thr71

Boldfaced residues correspond to SDPs accepted by consensus approach (see text); italicized residues are SDPs predicted by either Xdet or S3det in both alignments.