Schmid, Ralf;Gerloff, Dietlind L. - A Structural Model for NDH-2: Membrane Interaction and Function

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Title: A Structural Model for NDH-2: Membrane Interaction and Function	P146
Schmid, Ralf; Gerloff, Dietlind L. ralf@bch.ed.ac.uk Biocomputing Research Unit, ICMB, The University of Edinburgh

While respiratory complex I (NDH-1) is a proton-pumping multi-subunit protein complex, the alternative respiratory NADH-ubiquinone dehydrogenase (NDH-2) of E. coli is a single subunit enzyme bearing a non-covalently bound FAD as cofactor. NDH-2 is a membrane attached protein delivering electrons from NADH to the membrane quinone pool, and is hence particularly relevant to understand ubiquinone reduction sites and the interactions of proteins with biological membranes. Fold recognition by the 3D-PSSM server reveals a remote relationship of NDH-2 to members of the SCOP family "FAD/NADH-linked reductases" (alpha and beta proteins). Despite low over-all sequence identity (<20%) we were able to build a 3D-structural model for NDH-2, based on multiple templates using MODELLER 6v2. Mapping electrostatics on the surface of the model points to putative interaction sites with the membrane, the location of some conserved residues indicates a possible ubiquinone binding site.