5HBC

Intermediate structure of iron-saturated C-lobe of bovine lactoferrin at 2.79 Angstrom resolution indicates the softening of iron coordination

Summary for 5HBC

• Entry DOI: 10.2210/pdb5hbc/pdb
• Related: 4OQO
• Descriptor: Lactotransferrin, beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, FE (III) ION, ... (6 entities in total)
• Functional Keywords: c-lobe, lactoferrin, hydrolase
• Biological source: Bos taurus (Bovine)
• Total number of polymer chains: 2
• Total formula weight: 78489.69

Authors

Singh, A.,Rastogi, N.,Singh, P.K.,Tyagi, T.K.,Kaur, P.,Sharma, S.,Singh, T.P. (deposition date: 2015-12-31, release date: 2016-01-20, Last modification date: 2024-10-16)

Primary citation

Rastogi, N.,Singh, A.,Singh, P.K.,Tyagi, T.K.,Pandey, S.,Shin, K.,Kaur, P.,Sharma, S.,Singh, T.P.
Structure of iron saturated C-lobe of bovine lactoferrin at pH 6.8 indicates a weakening of iron coordination
Proteins, 84:591-599, 2016

PubMed Abstract: The bilobal lactoferrin is an approximately 76 kDa glycoprotein. It sequesters two Fe(3+) ions together with two CO(3)(2-) ions. The C-terminal half (residues, Tyr342-Arg689, C-lobe) of bovine lactoferrin (BLF) (residues Ala1-Arg689) was prepared by limited proteolysis using trypsin. Both C-lobe and intact BLF were saturated to 100%. Both of them retained up to nearly 85% of iron at pH 6.5. At pH 5.0, C-lobe retained 75% of iron whereas intact protein could retain only slightly more than 60%. At pH 4.0 both contained 25% iron and at pH 2.0 they were left with iron concentration of only 10%. The structure of iron saturated C-lobe was determined at 2.79 Å resolution and refined to R(cryst) and R(free) factors of 0.205 and 0.273, respectively. The structure contains two crystallographically independent molecules, A and B. They were found to have identical structures with an r.m.s. shift of 0.5 Å for their C(α) atoms. A high solvent content of 66% was observed in the crystals. The average value of an overall B-factor was 68.0 Å(2). The distance of 2.9 Å observed for the coordination bond between Fe(3+) ion and N(e2) of His595 appeared to be considerably longer than the normally observed values of 1.9-2.2 Å. This indicated that the coordination bond involving His595 may be absent. Other coordination distances were observed in the range of 2.1-2.3 Å. Based on the present structure of iron saturated C-lobe, it may be stated that His595 is the first residue to dissociate from ferric ion when the pH is lowered.

PubMed: 26850578
DOI: 10.1002/prot.25004

Experimental method

X-RAY DIFFRACTION (2.79 Å)