Cytochrome cd(1) structure: Unusual haem environments in a nitrite reductase and analysis of factors contributing to beta-propeller folds

The central tunnel of the eight-bladed beta-propeller domain of cytochrome cd(1) (nitrite reductase) is seen, from a 1.28 Angstrom, resolution structure, to contain hydrogen donors and accepters that are satisfied by interaction either with water or the d(1) haem. The d(1) haem, although bound by an extensive network of hydrogen bonds, is not distorted in its binding pocket and is confirmed to have exactly the dioxoisobacteriochlorin structure proposed from chemical studies. A biological rationale is advanced for the undistorted structure of the d(1) haem and the large number of hydrogen bonds it makes. The beta-propeller domain can be closely superimposed on that of methanol dehydrogenase despite the enzymes sharing no common sequence motifs and using a different set of interactions to ''Velcro'' close the propeller. The sequence and likely structural relationships between cytochrome cd(1) or methanol dehydrogenase and other predicted eight-bladed beta-propeller domains in proteins, such as the pyrolloquinoline quinone-dependent alcohol dehydrogenase, are discussed and compared with other propeller proteins. From sequencing the nirS gene of Thiosphaera pantotropha, it is established that the amino acid sequence deduced previously in part from X-ray diffraction data at lower resolution was largely correct, as was the proposal that eight N-terminal amino acid residues were not seen in the structure. The unusual haem iron environments in both the c-type cytochrome domain, with His/His coordination, and the d(1)-type cytochrome domain with Tyr/His coordination are related to the functions of the redox centres. (C) 1997 Academic Press Limited.