Structural studies on paired immunoglobulin-like receptor B and laspartomycin C

Abstract

Proteins are the universal molecular machines. From bacterial cell division to our own ability to see; interactions between proteins play a crucial role in biological processes in all kingdoms of life. Proteins carry out a mind-boggling array of functions; catalysis of chemical reactions, signaling, replication of DNA and even their own synthesis. All this complexity is created from only twenty different amino acids, linked together by peptide bonds to form a polypeptide chain. In almost all proteins this linear chain is twisted and turned to fold into a functional, well-defined three-dimensional structure. By elucidating these structures structural biology provides mechanistic insight at the molecular level into biologically, medically and technologically relevant processes. In this thesis I describe molecular and mechanistic insights into two biologically and medically important systems through the structures of PirB and laspartomycin C. Mouse PirB (paired immunoglobulin receptor B) and its human ortholog LILRB2 (leukocyte immunoglobulin-like receptor B2) are inhibitory receptors whose functions range from down regulation of immune response to inhibition of neuronal growth. In this thesis, we report the crystal structure of the PirB ectodomain; the first full ectodomain structures for a LILR family member. PirB's six Ig-like domains are arranged at acute angles, similar to leukocyte immunoglobulin-like receptor (LILR) and killer-cell immunoglobulin-like receptor (KIR) structures. This regular arrangement is followed throughout the ectodomain, resulting in an extended zigzag conformation. In two out of the five structures reported here, the repeating zigzag is broken by the first domain that can adopt two alternative orientations. Quantitative binding experiments reveal that PirB interacts with two structurally distinct ligands, oligodendrocyte myelin glycoprotein (OMgp) and myelin associated glycoprotein (MAG), through binding sites on the first four PirB Ig-like domains. Taken together, our structural and interaction data are compatible with a model for intercellular signaling in which PirB domains D1-D4, that are pointing away from the cell surface, enable interaction with ligands such as MAG and OMgp in trans. Laspartomycin C is a calcium-dependent antibiotic (CDA), CDAs are an important emerging class of antibiotics. In this thesis we report the crystal structure of the CDA laspartomycin C in complex with calcium and the ligand geranyl-phosphate at a resolution of 1.28 Å. This represents the first crystal structure of a CDA bound to its bacterial target. The structure is also the first to be reported for an antibiotic that binds the essential bacterial phospholipid undecaprenyl phosphate (C55-P). These structural insights are of great value in the design of antibiotics capable of exploiting this unique bacterial target.