Acevedo Morantes, Claudia Y.

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    In silico analysis of the putative CcmE protein from Rhodobacter sphaeroides 2.4.1
    (2007) Acevedo Morantes, Claudia Y.; Ramírez-Vick, Jaime E.; College of Arts and Sciences - Sciences; Martínez-Cruzado, Juan Carlos; Ríos-Velázquez, Carlos; Department of Biology; Pérez-Muñoz, Carlos A.
    Rhodobacter sphaeroides is a facultative photoheterotroph organism, belonging to the α-3 subdivision of the Proteobacteria. It has many modes of growth conferring advantage when the environmental conditions change. These different metabolic pathways involve a diversity of hemoproteins like cytochrome c2 (cyt c2). Within the cyt c2 maturation pathway a diversity of proteins is involved. CcmE is a chaperone protein involved in the covalent binding of a heme group through a histidine (H) residue, and delivering it to the CX2CH motif of the apo-cytochrome c2.. This study involves an in silico analysis of a hypothetical CcmE protein from Rhodobacter sphaeroides 2.4.1. Primers were designed based on the predicted ccmE gene sequence at GenBank and the translation was made using the ExPASy server. One hundred twenty-five CcmE sequences obtained from diverse organisms and related to CcmE from R. sphaeroides were used to generate a Multiple Sequence Alignment (MSA) using the ProbCons and T-Coffee applications. Two well conserved motifs Y*TGILPDLF*REG and LAKH*DE are found to be present in all sequences analyzed. A selection of conserved blocks from the MSA was used to generate a phylogenetic tree resulting in seven groups. The GEnt application found that tyrosine (Y*) and phenylalanine (F*) at the first motif and histidine (H*) at the second motif have the highest entropy score, implying a key functional role in the CcmE protein family. Finally, using the VMD application, the structure of the CcmE protein is compared: one from CcmE sequence obtained from in silico analysis against the CcmE obtained from the database of E. coli. All of these sequences have the six stranded β-sheet and histidine (H) and tyrosine (Y) residues iii involved in interactions between CcmE and the heme group. Our results for motifs of CCME_Rhodo are also in agreement with preliminary studies from CcmE obtained from database of E. coli. Our analysis suggest the presence of two well conserved motifs with internal gaps of variable length, consistent with previously published predictions. Using the predicted consensus sequences obtained from MEME analysis, we were able to predict the structure of CCME_Rhodo (obtained in silico) and compare it with the CcmE protein from E. coli (PDB ID 1SR3). These newly identified sequences are now more amenable for study using classic protein expression that may experimentally elucidate its structure and function.