03173nam a2200265 a 450000100080000000500110000800800410001910000190006024501140007926001800019330000190037350000200039252023290041265000190274165000110276065000110277165000140278265000160279665300200281265300100283265300120284265300140285470000190286870000200288715762432020-01-15       2009    bl uuuu     u00u1 u    #d1 aCAMINHA, I. P.  aStructural studies of Gluconate 5-dehydrogenase from gluconacetobacter diazotrophicus.h[electronic resource]  aIn: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 5., 2009, Angra dos Reis. Abstracts book... Angra dos Reis: ABBCBc2009  aNão paginado.  aX-Meeting 2009.  aThe recent sequencing of the Gluconacetobacter diazotrophicus genome, developed by Projeto RioGene, permits a search by ORFs related to organic acid production. In this study, a putative Gluconate 5-dehydrogenase (Ga5DH) ORF, A9H995, was selected. Ga5DH is an enzyme that plays an important role in regulating the flux of carbon and energy source in bacteria, and in the production of organic acids, among them the 5-keto-D-Gluconate (5KGA). Due to the fundamental role of this acid in the chemical industry, like the precursor to tartaric acid production for example, there is a large interest in respect to the structure of this protein since there is little physical or structural information available about it. To this end, we herein report the theoretical structure of Ga5DH from Gluconacetobacter diazotrophicus. This structure was obtained through in silico studies if the three-dimensional structure generated by homology modelling. The sequence alignment program BLAST was used to search homologous sequences against the Protein Data Bank (PDB), and the best template was chosen according to the sequence identity (ID). The reference structure used was the crystal structure of Ga5DH from Streptococcus suis species (PDB 3cxr:A). This protein wich belongs to the family of short-chain dehydrogenases/reductases (SDR), presented 42% identity with Ga5DH from G. diazotrophicus. By using the programa MODELLER9v6, ten models were built and the best model was determined by the lowest value of objective function. LIGPLOT was used to identify the interactions with possible ligants of this enzyme. A comparative analysis shows that the residues from S. Suis which are involved in ligand binding (GKR D-glucarate and NAP NADP Nicotinamide-adenine-dinucleotide-phosphate) are conserved both sequentially and structurally. This may suggests that the target sequence has the same ligands. Molecular dynamics simulations were performed with GROMACS software package. The residues involved in the interaction with the substrate were replaced by alanine, and the model with mutated amino acids was further submitted to molecular dynamics simulations to gain insights into affinities, contacts and stability of the essencial amino acids for structure and function of this enzyme, as well as information on the binding profile.  aBioinformatics  aModels  aGenoma  aProteína  aSimulação  aBioinformática  aBLAST  aGROMACS  aModelagem1 aFALCÃO, P. K.1 aTEIXEIRA, K. R.