PDBsum entry 1sdx

Transport protein

PDB id: 1sdx

Contents

Protein chain

335 a.a. *

Ligands

LEU-GLU-ALA-CYS-ALA

NAG-NDG

NAG-NDG-BMA-MAN-MAN-MAN

NAG-NAG-MAN

CO3

SO4

Metals

_ZN ×3

Waters ×228

* Residue conservation analysis

PDB id:

1sdx

Name:

Transport protein

Title:

Crystal structure of the zinc saturated c-terminal half of bovine lactoferrin at 2.0 a resolution reveals two additional zinc binding sites

Structure:

Lactotransferrin. Chain: a. Fragment: c-lobe. Synonym: lactoferrin. Mutation: yes. Lactotransferrin. Chain: e. Fragment: residues 681-685

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Secretion: mammary secretion. Secretion: mammary secretion

Resolution:

2.06Å R-factor: 0.192 R-free: 0.210

Authors:

T.Jabeen,S.Sharma,G.Singhal,N.Singh,T.P.Singh

Key ref:

T.Jabeen et al. (2005). Structure of the zinc-saturated C-terminal lobe of bovine lactoferrin at 2.0 A resolution. Acta Crystallogr D Biol Crystallogr, 61, 1107-1115. PubMed id: 16041076 DOI: 10.1107/S0907444905016069

Date:

15-Feb-04 Release date: 02-Mar-04

Protein chain

P24627  (TRFL_BOVIN) -  Lactotransferrin from Bos taurus

Seq: 708 a.a.

Struc: 335 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.4.21.- - ?????

DOI no: 10.1107/S0907444905016069

Acta Crystallogr D Biol Crystallogr 61:1107-1115 (2005)

PubMed id: 16041076

Structure of the zinc-saturated C-terminal lobe of bovine lactoferrin at 2.0 A resolution.

T.Jabeen, S.Sharma, N.Singh, A.Bhushan, T.P.Singh.

ABSTRACT

The crystal structure of the zinc-saturated C-terminal lobe of bovine lactoferrin has been determined at 2.0 A resolution using crystals stabilized at pH 3.8. This is the first metal-saturated structure of any functional lactoferrin at such a low pH. Purified samples of proteolytically generated zinc-saturated C-terminal lobe were crystallized from 0.1 M MES buffer pH 6.5 containing 25%(v/v) polyethyleneglycol monomethyl ether 550 and 0.1 M zinc sulfate heptahydrate. The crystals were transferred to 25 mM ammonium acetate buffer containing 25%(v/v) polyethyleneglycol monomethyl ether 550 and the pH was gradually changed from 6.5 to 3.8. The X-ray intensity data were collected with a 345 mm imaging-plate scanner mounted on an RU-300 rotating-anode X-ray generator using crystals soaked in the buffer at pH 3.8. The structure was determined with the molecular-replacement method using the coordinates of the monoferric C-terminal lobe of bovine lactoferrin as a search model and was refined to an R factor of 0.192 for all data to 2.0 A resolution. The final model comprises 2593 protein atoms (residues 342-676 and 681-685), 138 carbohydrate atoms (from 11 monosaccharide units in three glycan chains), three Zn2+ ions, one CO3(2-) ion, one SO(4)2- ions and 227 water molecules. The overall folding of the present structure is essentially similar to that of the monoferric C-terminal lobe of bovine lactoferrin, although it contains Zn2+ in place of Fe3+ in the metal-binding cleft as well as two additional Zn2+ ions on the surface of the C-terminal lobe. The Zn2+ ion in the cleft remains bound to the lobe with octahedral coordination. The bidentate carbonate ion is stabilized by a network of hydrogen bonds to Ala465, Gly466, Thr459 and Arg463. The other two zinc ions also form sixfold coordinations involving symmetry-related protein and water molecules. The number of monosaccharide residues from the three glycan chains of the C-terminal lobe was 11, which is the largest number observed to date. The structure shows that the C-terminal lobe of lactoferrin is capable of sequestering a Zn2+ ion at a pH of 3.8. This implies that the zinc ions can be sequestered over a wide pH range. The glycan chain attached to Asn545 may also have some influence on iron release from the C-terminal lobe.

Selected figure(s)

Figure 5.
Figure 5 A stereoview of a region of final (|2F[o] - F[c]|) electron-density map contoured at 1.5 [sigma] and the corresponding refined model. The diagram was produced using the program SwissPDBViewer (Guex & Peitsch, 1997 [Guex, N. & Peitsch, M. C. (1997). Electrophoresis, 18, 2714-2723.]-[bluearr.gif] ).

Figure 6.
Figure 6 Schematic representation of the C-terminal lobe. Three glycan chains linked to Asn368, Asn476 and Asn545 are shown in ball-and-stick representation. Three zinc ions, one in the metal-binding cleft (grey) and two at the surface (red), are shown. The C1 and C2 domains are also indicated. The hydrolyzed but C-C-linked fragment 681-685 is indicated as a CPK model.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 1107-1115) copyright 2005.

Figures were selected by an automated process.