Structure of copper- and oxalate-substituted human lactoferrin at 2.0 Å resolution

Smith, Clyde A.; Anderson, Bill; Baker, Heather M.; Baker, Edward N.

doi:10.1107/s0907444994000491

Cited by 21 publications

(24 citation statements)

References 29 publications

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“…These residues are located in y-turns in equivalent positions in the N-and C-lobes. Similar conformations at identical positions were observed in the RST and HLT structures (Smith, Anderson, Baker & Baker, 1994). This position is in the long loop connecting helix 9 and strand k which forms part of the interdomain contact.…”

Section: Fold Of the Polypeptide Chainsupporting

confidence: 74%

Structure of Diferric Duck Ovotransferrin at 2.35 Å Resolution

Rawas

Muirhead²,

Williams³

1996

Acta Cryst D

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The structure of diferric duck ovotransferrin (DOT) has been determined and refined at a resolution of 2.35 A. The DOT structure, which contains two iron binding sites, is similar to the known transferrin and lactoferrin structures. The two iron-binding sites, one in the Nterminal lobe and one in the C-terminal lobe of the molecule, are similar but not identical. The main differences between the three known structures lie in the relative orientations of the N-and C-lobes with respect to each other. In the DOT structure the large aromatic side chain of Phe322 in the N-lobe packs against the conserved residue Gly387 in the C-lobe. This interaction is at the centre of the interface between the two lobes and could play a crucial role in determining their relative orientation. Other differences between the structures occur in the surface loops and in the peptide connecting the two lobes. The final crystallographic model consists of 5309 protein atoms (686 residues), two Fe 3+ ions, two (bi)carbonate ions and three carbohydrate moities. 318 water molecules have been added to the model. The final R factor is 0.22 for 25400 observed reflections between 10 and 2.35A resolution. I. AbbreviationsDOT, duck ovotransferrin; HOT, hen ovotransferrin; HST, human serum transferrin; HMT, human melanotransferrin; RST, rabbit serum transferrin; HLT, human lactoferrin; MLT, mouse lactoferrin; MST, Manduca sexta transferrin; r.m.s., root-mean-square; NAG, N-acetylglucosamine; FUC, fucose.

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Section: Fold Of the Polypeptide Chainsupporting

confidence: 74%

Structure of Diferric Duck Ovotransferrin at 2.35 Å Resolution

Rawas

Muirhead²,

Williams³

1996

Acta Cryst D

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“…A synergistic ion, CO 3 2− , is easily replaced by oxalate at the N-site of serum transferrin or at the C-site of lactoferrin. 7,8) These results show that the two metal binding sites (N-and C-sites) in transferrin are not equivalent.Further crystallographic and point mutation studies of the recombinant N-lobe of human serum-Tf have shown that the position of Arg124 that formed a hydrogen bond with the synergistic carbonate ion changes dramatically as the coordination geometry of the N-site changes 9,10) and that Arg124 plays an important role in the iron release rate.10,11) Arg124* To whom correspondence should be addressed. e-mail: hata@fupharm.fukuyama-u.ac.jp N-and C-lobes are shown by a ribbon model.…”

mentioning

confidence: 85%

mentioning

confidence: 85%

Flexibility of the Coordination Geometry at the N-Site of Cu(II)<sub>2</sub> Human Serum-Transferrin Induced by the Different Orientations of Arg124

Hata

Shibata

Okano

et al. 2015

Biological & Pharmaceutical Bulletin

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The ESR spectra of dicupric human serum-transferrin (serum-Tf) were measured from 20 to 37°C in the liquid state (56% glycerol at pH 7.6). Two coordination geometries (types B-1 and B-2) with different ESR parameters were present at the N-site. The contents of the coordination geometry of type B-1 at the N-site increased as the temperature increased. The equilibrium constant between the coordination geometries of types B-1 and B-2 was determined by ESR spectra. The enthalpy value from type B-2 to B-1 was 5.3 kcal/mol, as obtained from a van't Hoff plot. The two conformational energies of the cluster models of the copper-binding site at the N-site of dicupric human serum-Tf, where the Arg124 residue was oriented in two different directions (conformations I and II), were calculated by Density Functional Theory, and the enthalpy value from conformation II to I was 2.1 kcal/mol. The enthalpy value was similar to that ( 5.3 kcal/ mol) obtained by the coordination geometrical change from type B-2 to B-1 in Cu(II) 2 serum-Tf. In conformations I and II, the residue of Arg124 at the N-site is located either far from or near the copper-binding site, respectively, and in both cases the coordination geometry of the cupric ions at the N-site has changed from a flattened tetrahedron to a trigonal bipyramid. This result implies that the ESR spectral change from type B-2 to B-1 is caused by the presence of two different orientations of Arg124 in the change from conformation II to I. Key words copper transferrin; conformational change energy; coordination geometry change Transferrins (Tfs), a group of homologous iron-binding proteins (serum-transferrin (serum-Tf), ovo-transferrin (ovoTf), and lactoferrin (Lf)), consist of a single polypeptide chain folded into two lobes. Tfs are composed of homologous lobes. The amino-terminal half of these proteins forms one lobe (N-lobe), linked by a short peptide sequence to the carboxyterminal lobe (C-lobe) as shown in Fig. 1. 1) Each lobe is comprised of two domains that open and close with a hinge motion. The metal binding sites are located deep at these clefts in the N-and C-lobes, and the metal binding sites of these lobes are expressed as N-and C-sites, respectively. Crystallographic studies on Fe(III) 2 human serum-Tf, 2) Fe(III) 2 human Lf, 3) and Fe(III) 2 ovo-Tf 4) have demonstrated that the iron coordination is similar for these proteins, with the metal bound to four protein ligands (two Tyr, one Asp, and one His) and a CO 3 2− (bidentate) anion, and that the coordination geometries of the two specific sites in each protein are essentially equivalent. However, Harris 5,6) reported that the metal binding constants of various metal ions at the C-and N-sites are different and that the metal binding constant at the C-site is generally much larger than that of the N-site. A synergistic ion, CO 3 2− , is easily replaced by oxalate at the N-site of serum transferrin or at the C-site of lactoferrin. 7,8) These results show that the two metal binding sites (N-and C-sites) in transferrin are...

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“…In the transferase, thiaminase I, 43 the ligand molecule is packed at the cleft between two sub-domains, while the hydrolase, lactoferrin, 44 is supposed to bind the ligand on the surface of one sub-domain, located far from the cleft [ Fig. 3(c)].…”

Section: Other Strategiesmentioning

confidence: 99%

“…3(a)]. In the ''ribonuclease 43 and the hydrolase, lactoferrin (PDB: 1lcf, chain A), 44 of the ''periplasmic binding protein-like II'' (c.94.1) superfamily. In the transferase, the catalytic sites (C113 and E241, blue CPK) are in the middle (red circle) of the two sub-domains (9-113 and 270-354 in green, 114-269 and 355-370 in cyan).…”

Section: Other Strategiesmentioning

confidence: 99%

Alteration of oligomeric state and domain architecture is essential for functional transformation between transferase and hydrolase with the same scaffold

2009

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Transferases and hydrolases catalyze different chemical reactions and express different dynamic responses upon ligand binding. To insulate the ligand molecule from the surrounding water, transferases bury it inside the protein by closing the cleft, while hydrolases undergo a small conformational change and leave the ligand molecule exposed to the solvent. Despite these distinct ligand-binding modes, some transferases and hydrolases are homologous. To clarify how such different catalytic modes are possible with the same scaffold, we examined the solvent accessibility of ligand molecules for 15 SCOP superfamilies, each containing both transferase and hydrolase catalytic domains. In contrast to hydrolases, we found that nine superfamilies of transferases use two major strategies, oligomerization and domain fusion, to insulate the ligand molecules. The subunits and domains that were recruited by the transferases often act as a cover for the ligand molecule. The other strategies adopted by transferases to insulate the ligand molecule are the relocation of catalytic sites, the rearrangement of secondary structure elements, and the insertion of peripheral regions. These findings provide insights into how proteins have evolved and acquired distinct functions with a limited number of scaffolds.

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Structure of copper- and oxalate-substituted human lactoferrin at 2.0 Å resolution

Cited by 21 publications

References 29 publications

Structure of Diferric Duck Ovotransferrin at 2.35 Å Resolution

Structure of Diferric Duck Ovotransferrin at 2.35 Å Resolution

Flexibility of the Coordination Geometry at the N-Site of Cu(II)<sub>2</sub> Human Serum-Transferrin Induced by the Different Orientations of Arg124

Alteration of oligomeric state and domain architecture is essential for functional transformation between transferase and hydrolase with the same scaffold

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