9XXU

Crystal structure of the chymotrypsin-cleaved iron-free C-lobe of bovine lactoferrin at 2.82 Angstrom resolution

Summary for 9XXU

• Entry DOI: 10.2210/pdb9xxu/pdb
• Descriptor: Lactotransferrin, C-terminal fragment of Lactotransferrin, alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (10 entities in total)
• Functional Keywords: c-lobe, lactoferrin, iron binding, clf, metal binding protein
• Biological source: Bos taurus (domestic cattle); More
• Total number of polymer chains: 4
• Total formula weight: 80799.14

Authors

Pandit, S.,Ahmad, N.,Sharma, P.,Sharma, S.,Singh, T.P. (deposition date: 2025-12-01, release date: 2025-12-31, Last modification date: 2026-09-16)

Primary citation

Pandit, S.,Ahmad, N.,Sharma, P.,Sharma, S.,Singh, T.P.
Structural Basis for Single-Site Cleavage of Lactoferrin by Diverse Proteases for Prolonged Antibacterial Action: Structure of the Chymotrypsin-Cleaved Lactoferrin C-Lobe.
Proteins, 94:1658-1670, 2026

PubMed Abstract: The stable lactoferrin C-lobe offers strong potential for therapeutic applications as an antibacterial agent. Lactoferrin is a 78 kDa (Ala1Arg689) iron-binding glycoprotein which is composed of two homologous N- and C-lobes, connected by an 11-residue α-helical linker (Thr334Arg344). The limited proteolysis of lactoferrin, carried out using chymotrypsin, generated a 40 kDa, fully functional C-lobe. The structure determination revealed that the protein chain consisted of residues from Thr343 to Leu680 together with a disulfide-linked tripeptide, Ala683Cys684Ala685. It showed that the cleavage occurred specifically at the Tyr342Thr343 peptide bond within the inter-lobe 11-residue-long peptide. Remarkably, previous studies using proteinase K, trypsin, and pepsin also produced an identical C-lobe. Thus, the inter-lobe region seems to be stereochemically designed by nature for the single-site cleavage by multiple digestive enzymes. The proteolytically generated C-lobe, with three observed glycosylation sites, remains stable for 3 days in the presence of digestive enzymes. The stable C-lobe continues to sequester iron, thus showing a prolonged antibacterial property. This is a unique example of evolutionary convergence whereby multiple digestive enzymes cleave a native protein into a stable half molecule with full antibacterial action.

PubMed: 42230792
DOI: 10.1002/prot.70148

Experimental method

X-RAY DIFFRACTION (2.82 Å)