Computational protocol: Catalytic Mechanism of Short Ethoxy Chain Nonylphenol Dehydrogenase Belonging to a Polyethylene Glycol Dehydrogenase Group in the GMC Oxidoreductase Family

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Protocol publication

[…] There are two structurally defined homologues of NPEO-DH, OPEO-DH and PEGDH: GOX (EC 1.1.3.4) from A. niger (Protein Data Base (PDB) code: 1cf3, 25% identity with NPEO-DH) and GOX (EC 1.1.3.4) from P. amagasakiense (PDB code: 1gpe, 26% identity with NPEO-DH) []. MODELLER Release 9v7 (developed by Sali and Blundell []) was used for modeling. We chose 1cf3 as the structure template because it yielded fewer gaps than when 1gpe was used as the template. As MODELLER does not have energy parameters for FAD, an FAD molecule was modeled using the “block” residue option, under the restraint that it conformed to the template structure. Ohta et al. [] reported the validity of GOX as a template for 3D structure modeling. PSI-BLAST [] was used to align NPEO-DH (DQ368396) with OPEO-DH (AB100375) and PEG-DH (AB050784). […]

Pipeline specifications

Software tools MODELLER, BLASTP
Application Protein structure analysis
Organisms Pseudomonas putida
Diseases Glucose Intolerance
Chemicals Choline, Flavin-Adenine Dinucleotide, Glucose, Polyethylene Glycols