TY - JOUR
T1 - Homology modeling of the structure of acyl coA:isopenicillin N-acyltransferase (IAT) from Penicillium chrysogenum. IAT interaction studies with isopenicillin-N, combining molecular dynamics simulations and docking
AU - Moreno-Vargas, Liliana
AU - Correa-Basurto, Jose
AU - Maroun, Rachid C.
AU - Fernández, Francisco J.
N1 - Funding Information:
The investigation was supported in part by grants from the Consejo Nacional de Ciencia y Tecnología (CONACyT), Mexico (Grant No. 132353), and Instituto Politécnico Nacional (Secretaría de Investigación y Posgrado and Comisión de Operación y Fomento de Actividades Académicas) and Instituto de Ciencia y Tecnología del Distrito Federal.
PY - 2012/3
Y1 - 2012/3
N2 - In the last step of penicillin biosynthesis, acyl- CoA:isopenicillin N acyltransferase (IAT) (E.C. 2.3.1.164) catalyzes the conversion of isopenicillin N (IPN) to penicillin G. IAT substitutes the α-aminoadipic acid side chain of IPN by a phenylacetic acid phenolate group (from phenylacetyl-CoA). Having a three-dimensional (3D) structure of IAT helps to determine the steps involved in side chain exchange by identifying the atomic details of substrate recognition. We predicted the IAT 3-D structure (α- and β-subunits), as well as the manner of IPN and phenylacetyl-CoA bind to the mature enzyme (β-subunit). The 3D IAT prediction was achieved by homology modeling and molecular docking in different snapshots, and refined by molecular dynamic simulations. Our model can reasonably interpret the results of a number of experiments, where key residues for IAT processing as well as strictly conserved residues most probably involved with enzymatic activity were mutated. Based on the results of docking studies, energies associated with the complexes, and binding constants calculated, we identified a site located in the region generated by β1, β2 and β5 strands, which forms part of the central structure of β-subunit, as the potential binding site of IPN. The site comprises the amino acid residues Cys103, Asp121, Phe122, Phe123, Ala168, Leu169, His170, Gln172, Phe212, Arg241, Leu262, Asp264, Arg302, Ser309, and Arg310. Through hydrogen bonds, the IPN binding site establishes interactions with Cys103, Leu169, Gln172, Asp264 and Arg310. Our model is also validated by a recently revealed crystal structure of the mature enzyme.
AB - In the last step of penicillin biosynthesis, acyl- CoA:isopenicillin N acyltransferase (IAT) (E.C. 2.3.1.164) catalyzes the conversion of isopenicillin N (IPN) to penicillin G. IAT substitutes the α-aminoadipic acid side chain of IPN by a phenylacetic acid phenolate group (from phenylacetyl-CoA). Having a three-dimensional (3D) structure of IAT helps to determine the steps involved in side chain exchange by identifying the atomic details of substrate recognition. We predicted the IAT 3-D structure (α- and β-subunits), as well as the manner of IPN and phenylacetyl-CoA bind to the mature enzyme (β-subunit). The 3D IAT prediction was achieved by homology modeling and molecular docking in different snapshots, and refined by molecular dynamic simulations. Our model can reasonably interpret the results of a number of experiments, where key residues for IAT processing as well as strictly conserved residues most probably involved with enzymatic activity were mutated. Based on the results of docking studies, energies associated with the complexes, and binding constants calculated, we identified a site located in the region generated by β1, β2 and β5 strands, which forms part of the central structure of β-subunit, as the potential binding site of IPN. The site comprises the amino acid residues Cys103, Asp121, Phe122, Phe123, Ala168, Leu169, His170, Gln172, Phe212, Arg241, Leu262, Asp264, Arg302, Ser309, and Arg310. Through hydrogen bonds, the IPN binding site establishes interactions with Cys103, Leu169, Gln172, Asp264 and Arg310. Our model is also validated by a recently revealed crystal structure of the mature enzyme.
KW - Acyl-CoA: isopenicillin-N acyltransferase
KW - Homology modeling
KW - Ligand binding-site
KW - Long-term molecular dynamic simulations
KW - Molecular docking
KW - Penicillin biosynthesis
KW - Protein-ligand interaction
UR - http://www.scopus.com/inward/record.url?scp=84861333084&partnerID=8YFLogxK
U2 - 10.1007/s00894-011-1143-z
DO - 10.1007/s00894-011-1143-z
M3 - Artículo
C2 - 21695507
SN - 1610-2940
VL - 18
SP - 1189
EP - 1205
JO - Journal of Molecular Modeling
JF - Journal of Molecular Modeling
IS - 3
ER -