3T1D

The mutant structure of human Siderocalin W79A, R81A, Y106F bound to Enterobactin

Summary for 3T1D

• Entry DOI: 10.2210/pdb3t1d/pdb
• Related: 3TF6 3TZS 3U03 3U0D
• Descriptor: Neutrophil gelatinase-associated lipocalin, GLYCEROL, CHLORIDE ION, ... (8 entities in total)
• Functional Keywords: ssgcid, seattle structural genomics center for infectious disease, beta-barrel, siderocalin, w79a, r81a, y106f, antimicrobial protein
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 3
• Total formula weight: 68857.95

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID) (deposition date: 2011-07-21, release date: 2011-08-17, Last modification date: 2025-10-22)

Primary citation

Clifton, M.C.,Rupert, P.B.,Hoette, T.M.,Raymond, K.N.,Abergel, R.J.,Strong, R.K.
Parsing the functional specificity of Siderocalin/Lipocalin 2/NGAL for siderophores and related small-molecule ligands.
J Struct Biol X, 2:100008-100008, 2019

PubMed Abstract: Siderocalin/Lipocalin 2/Neutrophil Gelatinase Associated Lipocalin/24p3 is an innate immune system protein with bacteriostatic activity, acting by tightly binding and sequestering diverse catecholate and mixed-type ferric siderophores from enteric bacteria and mycobacteria. Bacterial virulence achieved through siderophore modifications, or utilization of alternate siderophores, can be explained by evasion of Siderocalin binding. Siderocalin has also been implicated in a wide variety of disease processes, though often in seemingly contradictory ways, and has been proposed to bind to a broader array of ligands beyond siderophores. Using structural, directed mutational, and binding studies, we have sought to rigorously test, and fully elucidate, the Siderocalin recognition mechanism. Several proposed ligands fail to meet rigorous binding criteria, including the bacterial siderophore pyochelin, the iron-chelating catecholamine hormone norepinephrine, and the bacterial second messenger cyclic diguanylate monophosphate. While possessing a remarkably rigid structure, in principle simplifying analyses of ligand recognition, understanding Scn recognition is complicated by the observed conformational and stoichiometric plasticity, and instability, of its siderophore ligands. Since the role of Siderocalin at the early host/pathogen interface is to compete for bacterial ferric siderophores, we also analyzed how bacterial siderophore binding proteins and enzymes alternately recognize siderophores that efficiently bind to, or evade, Siderocalin sequestration - including determining the crystal structure of YfiY bound to schizokinen. These studies combine to refine the potential physiological functions of Siderocalin by defining its multiplexed recognition mechanism.

PubMed: 32647813
DOI: 10.1016/j.yjsbx.2019.100008

Experimental method

X-RAY DIFFRACTION (2.3 Å)