PDBsum entry 1nft

Transport protein

PDB id: 1nft

Contents

Protein chain

329 a.a. *

Ligands

SO4 ×3

NTA

Metals

_FE

Waters ×153

* Residue conservation analysis

PDB id:

1nft

Name:

Transport protein

Title:

Ovotransferrin, n-terminal lobe, iron loaded open form

Structure:

Protein (ovotransferrin). Chain: a. Fragment: n-terminal lobe

Source:

Gallus gallus. Chicken. Organism_taxid: 9031. Organ: egg

Biol. unit:

Hexamer (from PQS)

Resolution:

2.10Å R-factor: 0.189 R-free: 0.256

Authors:

K.Mizutani,H.Yamashita,H.Kurokawa,B.Mikami,M.Hirose

Key ref:

K.Mizutani et al. (1999). Alternative structural state of transferrin. The crystallographic analysis of iron-loaded but domain-opened ovotransferrin N-lobe. J Biol Chem, 274, 10190-10194. PubMed id: 10187803 DOI: 10.1074/jbc.274.15.10190

Date:

07-Jan-99 Release date: 13-Jan-99

Protein chain

P02789  (TRFE_CHICK) -  Ovotransferrin from Gallus gallus

Seq: 705 a.a.

Struc: 329 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DOI no: 10.1074/jbc.274.15.10190

J Biol Chem 274:10190-10194 (1999)

PubMed id: 10187803

Alternative structural state of transferrin. The crystallographic analysis of iron-loaded but domain-opened ovotransferrin N-lobe.

K.Mizutani, H.Yamashita, H.Kurokawa, B.Mikami, M.Hirose.

ABSTRACT

Transferrins bind Fe3+ very tightly in a closed interdomain cleft by the coordination of four protein ligands (Asp60, Tyr92, Tyr191, and His250 in ovotransferrin N-lobe) and of a synergistic anion, physiologically bidentate CO32-. Upon Fe3+ uptake, transferrins undergo a large scale conformational transition: the apo structure with an opening of the interdomain cleft is transformed into the closed holo structure, implying initial Fe3+ binding in the open form. To solve the Fe3+-loaded, domain-opened structure, an ovotransferrin N-lobe crystal that had been grown as the apo form was soaked with Fe3+-nitrilotriacetate, and its structure was solved at 2.1 A resolution. The Fe3+-soaked form showed almost exactly the same overall open structure as the iron-free apo form. The electron density map unequivocally proved the presence of an iron atom with the coordination by the two protein ligands of Tyr92-OH and Tyr191-OH. Other Fe3+ coordination sites are occupied by a nitrilotriacetate anion, which is stabilized through the hydrogen bonds with the peptide NH groups of Ser122, Ala123, and Gly124 and a side chain group of Thr117. There is, however, no clear interaction between the nitrilotriacetate anion and the synergistic anion binding site, Arg121.

Selected figure(s)

Figure 2.
Fig. 2. Stereo C[ ]plots of apo (black) and Fe^3+-soaked (cyan) and holo forms (red) of ovotransferrin N-lobe. The figures are produced with MOLSCRIPT (30) and Raster3D (31) as the superimposed ones on domain N2. The holo (Fe^3+- and CO[3]^2 -loaded ovotransferrin N-lobe) structure is drawn using the previous data (8). The apo structure of ovotransferrin N-lobe is the one employed as the model for the current structural determination of the Fe^3+-soaked form (see "Experimental Procedures"). The residue numbers are labeled for the Fe^3+-soaked form. The iron atom (green sphere) and the side chains (blue) of His^250, Asp^60, Tyr^92, and Tyr^191 (from top to bottom in this order) for the Fe^3+-soaked form are also displayed.

Figure 3.
Fig. 3. Stereo views depicting the iron binding site in the Fe^3+-soaked form. a, electron density maps (green: 2Fo Fc, contoured at 1 ; blue: Fo Fc, contoured at 3 ) obtained using the reflection data of the Fe^3+-soaked form after refinement of the model in which the NTA molecule was omitted. b, anomalous difference Fourier density map contoured at 3 (purple) calculated with exclusion of an iron atom using the reflection data of the Fe^3+-soaked form at 7.0-2.1 Å. The final model is superimposed in stick presentation with atoms in standard colors.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (1999, 274, 10190-10194) copyright 1999.

Figures were selected by an automated process.