The crystal structure of human α₁-microglobulin reveals a potential haem-binding site

We describe the 2.3 Å (1 Å=0.1 nm) X-ray structure of α₁m (α₁-microglobulin), an abundant protein in human blood plasma, which reveals the β-barrel fold typical for lipocalins with a deep pocket lined by four loops at its open rim. Loop #1 harbours the residue Cys³⁴ which is responsible for covalent cross-linking with plasma IgA. A single disulfide bond between Cys⁷² and Cys¹⁶⁹ connects the C-terminal segment to the β-barrel, as in many other lipocalins. The exposed imidazole side chains of His¹²² and His¹²³ in loop #4 give rise to a double Ni²⁺-binding site together with a crystallographic neighbour. The closest structural relatives of α₁m are the complement protein component C8γ, the L-prostaglandin D synthase and lipocalin 15, three other structurally characterized members of the lipocalin family in humans that have only distant sequence similarity. In contrast with these, α₁m is initially expressed as a bifunctional fusion protein with the protease inhibitor bikunin. Neither the electron density nor ESI–MS (electrospray ionization MS) provide evidence for a chromophore bound to the recombinant α₁m, also known as ‘yellow/brown lipocalin’. However, the three side chains of Lys⁹², Lys¹¹⁸ and Lys¹³⁰ that were reported to be involved in covalent chromophore binding appear to be freely accessible to ligands accommodated in the hydrophobic pocket. A structural feature similar to the well-known Cys–Pro haem-binding motif indicates the presence of a haem-binding site within the loop region of α₁m, which explains previous biochemical findings and supports a physiological role in haem scavenging, as well as redox-mediated detoxification.