International Journal of Biological Macromolecules 48 (2011) 466–473 Contents lists available at ScienceDirect International Journal of Biological Macromolecules journal homepage: www.elsevier.com/locate/ijbiomac Comparative structural modeling and docking studies of oxalate oxidase: Possible implication in enzyme supplementation therapy for urolithiasis C.N. Khobragade a,∗ , Supriya D. Beedkar a , Ragini G. Bodade a , Aruna S. Vinchurkar b a School of Life sciences: Swami Ramanand Teerth Marathwada University, Nanded 431606, India b Department of Biophysics, Institute of Science, Aurangabad 415570, India article info Article history: Received 30 October 2010 Received in revised form 8 January 2011 Accepted 10 January 2011 Available online 19 January 2011 Keywords: Homology modeling Oxalate Automated docking Structure function relationship Region-specificity of enzyme abstract In humans oxalate is end product of protein metabolism, with no enzyme present to act on it. In conditions of its enhanced endogenous synthesis or increased absorption from the diet, oxalate accumulation leads to hyperoxaluria which can further lead to a number of pathological conditions including urolithiasis. Urolithiasis has been a perplexing problem due to its high incidence and rate of recurrence after treat- ment like Extracorporeal-shock wave lithotripsy (ESWL). Hence other prophylactic treatment becomes necessary. One of the newer approaches of curing such metabolic disorders is the enzyme supplemen- tation therapy. Oxalate oxidase (OxOx) is a commonly occurring enzyme in plants, bacteria and fungi that catalyses oxidative cleavage of oxalate to CO 2 with reduction of dioxygen to H 2 O 2 . Present study, used Hordeum vulgare OxOx crystal structure (PDB ID 2ET1A) as a template for constructing 3D models of OxOx from Triticum aestivum, Arabidopsis thaliana, Sclerotiana sclerotiarum. Similarly Homology models for isoforms Ceriporiopsis subvermispora 336, C. subvermispora 422 were constructed by using template Bacillus subtilis oxalate decarboxylase (Oxdc) (PDB ID 2UY8A) by comparative modeling approach in SWISS MODEL, MODELLER, 3D JIGSAW and GENO 3D program server. Based on overall stereochemi- cal quality (PROCHECK, PROSA, VARIFY 3D), best models were selected, energy minimized, refined and characterized for active site in BioMed CaChe V 6.1 workspace. Selected models were further studied for structure function relationship with substrate (oxalate) and its analogue (glycolate) by using dock- ing approach. Calculated interaction energy between the oxalate and constructed enzyme indicated that homology models for OxOx of T. aestivum, A. thaliana and S. sclerotiarum, can account for better regio- specificity of this enzyme towards oxalate. That supports the interested metabolism and thus may further implement in enzyme supplementation therapy for urolithiasis. Published by Elsevier B.V. 1. Introduction Oxalate oxidase (OxOx EC 1.2.3.4), a metalloflavoprotein catal- yses the oxidative cleavage of oxalate to CO 2 with reduction of dioxygen to H 2 O 2 [1–4]. It is widely distributed in nature and has been found in bacteria [5] fungi [6] and various plant tissues. In plants germins and germin like proteins (GLP’s) belonging to cupin superfamily has been identified as an oxalate oxidase in the embryos of cereal seeds during germination. Structurally germins are hexamer glycoprotein with Mn containing group [7,8]. Germin family proteins have been widely studied in crop plants due to their diverse role against invading pathogens producing oxalate during pathogenesis. It also regulates release of Ca ++ and H 2 O 2 as two important signal molecules in plants [9]. Oxalate degrading capa- bility of present enzyme is a matter of interest for present study. ∗ Corresponding author. Fax: +91 2462229572. E-mail address: cnkhobragade@rediffmail.com (C.N. Khobragade). Oxalate a product of protein metabolism, is excreted by kidney. In case of high endogenous production and dietary intake it accumu- lates instead, forming insoluble complexes with divalent cations mainly calcium. Deposition of such insoluble complexes leads to medical complications including hyperoxaluria, urolithiasis, renal failure, cardiomyopathy and cardiac conductance disorder [10,11]. Out of these, urolithiasis has been perplexing problem worldwide affecting about 1% Americans each year. Thiazides and indapamide are medically prescribed drugs for treatment of urolithiasis. Use of these drugs is limited by associated side effects such as hypoten- sion, impotence, muscular cramps, asthenia, hypokalamia and hypercholesteromia. Use of Extracorporeal-shock wave lithotripsy (ESWL) method for removal of stone is associated with chances of recurrences [12]. Use of enzyme supplementation therapy there- fore may prove to be promising therapy against all complications including urolithiasis [11]. An important aspect to screen enzymes for enzyme supplemen- tation therapy is the study of structure and function relationship of catabolic enzymes. Such studies provide insight into the molecu- 0141-8130/$ – see front matter. Published by Elsevier B.V. doi:10.1016/j.ijbiomac.2011.01.007