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PDBsum entry 1a8f
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Iron transport
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PDB id
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1a8f
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Contents |
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* Residue conservation analysis
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PDB id:
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| Name: |
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Iron transport
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Title:
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Human serum transferrin, recombinant n-terminal lobe
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Structure:
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Serum transferrin. Chain: a. Fragment: n-terminal lobe. Engineered: yes
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Cell_line: baby hamster kidney cells. Organ: kidney. Expressed in: cricetinae. Expression_system_taxid: 10026.
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Resolution:
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1.80Å
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R-factor:
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0.202
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R-free:
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0.250
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Authors:
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R.T.A.Macgillivray,S.A.Moore,J.Chen,B.F.Anderson,H.Baker,Y.Luo, M.Bewley,C.A.Smith,M.E.P.Murphy,Y.Wang,A.B.Mason,R.C.Woodworth, G.D.Brayer,E.N.Baker
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Key ref:
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R.T.MacGillivray
et al.
(1998).
Two high-resolution crystal structures of the recombinant N-lobe of human transferrin reveal a structural change implicated in iron release.
Biochemistry,
37,
7919-7928.
PubMed id:
DOI:
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Date:
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25-Mar-98
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Release date:
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17-Jun-98
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PROCHECK
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Headers
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References
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P02787
(TRFE_HUMAN) -
Serotransferrin from Homo sapiens
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Seq:
Struc:
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698 a.a.
329 a.a.
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Key: |
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Secondary structure |
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CATH domain |
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DOI no:
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Biochemistry
37:7919-7928
(1998)
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PubMed id:
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Two high-resolution crystal structures of the recombinant N-lobe of human transferrin reveal a structural change implicated in iron release.
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R.T.MacGillivray,
S.A.Moore,
J.Chen,
B.F.Anderson,
H.Baker,
Y.Luo,
M.Bewley,
C.A.Smith,
M.E.Murphy,
Y.Wang,
A.B.Mason,
R.C.Woodworth,
G.D.Brayer,
E.N.Baker.
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ABSTRACT
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The N-lobe of human serum transferrin (hTF/2N) has been expressed in baby
hamster kidney cells and crystallized in both orthorhombic (P212121) and
tetragonal (P41212) space groups. Both crystal forms diffract to high resolution
(1.6 and 1.8 A, respectively) and have been solved by molecular replacement.
Subsequent refinement resulted in final models for the structure of hTF/2N that
had crystallographic R-factors of 18.1 and 19.7% for the two crystal forms,
respectively; these models represent the highest-resolution transferrin
structures determined to date. The hTF/2N polypeptide has a folding pattern
similar to those of other transferrins, including the presence of a deep cleft
that contains the metal-binding site. In contrast to other transferrins, both
crystal forms of hTF/2N display disorder at the iron-binding site; model
building suggests that this disorder consists of alternative conformations of
the synergistically bound carbonate anion, the side chain for Arg-124, and
several solvent molecules. Subsequent refinement revealed that conformation A
has an occupancy of 0.63-0. 65 and corresponds to the structure of the
iron-binding site found in other transferrins. The alternative conformation B
has an occupancy of 0.35-0.37; in this structure, the carbonate has rotated 30
degrees relative to the iron and the side chain for Arg-124 has moved to
accommodate the new carbonate position. Several water molecules appear to
stabilize the carbonate anion in the two conformations. These structures are
consistent with the protonation of the carbonate and resulting partial removal
of the anion from the metal; these events would occur prior to cleft opening and
metal release.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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F.I.Staquicini,
M.G.Ozawa,
C.A.Moya,
W.H.Driessen,
E.M.Barbu,
H.Nishimori,
S.Soghomonyan,
L.G.Flores,
X.Liang,
V.Paolillo,
M.M.Alauddin,
J.P.Basilion,
F.B.Furnari,
O.Bogler,
F.F.Lang,
K.D.Aldape,
G.N.Fuller,
M.Höök,
J.G.Gelovani,
R.L.Sidman,
W.K.Cavenee,
R.Pasqualini,
and
W.Arap
(2011).
Systemic combinatorial peptide selection yields a non-canonical iron-mimicry mechanism for targeting tumors in a mouse model of human glioblastoma.
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J Clin Invest,
121,
161-173.
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T.Oroguchi,
and
M.Ikeguchi
(2011).
Effects of ionic strength on SAXS data for proteins revealed by molecular dynamics simulations.
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J Chem Phys,
134,
025102.
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B.E.Eckenroth,
A.B.Mason,
M.E.McDevitt,
L.A.Lambert,
and
S.J.Everse
(2010).
The structure and evolution of the murine inhibitor of carbonic anhydrase: a member of the transferrin superfamily.
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Protein Sci,
19,
1616-1626.
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PDB code:
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G.L.Butterfoss,
E.F.Derose,
S.A.Gabel,
L.Perera,
J.M.Krahn,
G.A.Mueller,
X.Zheng,
and
R.E.London
(2010).
Conformational dependence of (13)C shielding and coupling constants for methionine methyl groups.
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J Biomol NMR,
48,
31-47.
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H.K.Khambati,
T.F.Moraes,
J.Singh,
S.R.Shouldice,
R.H.Yu,
and
A.B.Schryvers
(2010).
The role of vicinal tyrosine residues in the function of Haemophilus influenzae ferric-binding protein A.
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Biochem J,
432,
57-64.
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PDB codes:
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M.E.Brandsma,
H.Diao,
X.Wang,
S.E.Kohalmi,
A.M.Jevnikar,
and
S.Ma
(2010).
Plant-derived recombinant human serum transferrin demonstrates multiple functions.
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Plant Biotechnol J,
8,
489-505.
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N.G.James,
J.A.Ross,
A.B.Mason,
and
D.M.Jameson
(2010).
Excited-state lifetime studies of the three tryptophan residues in the N-lobe of human serum transferrin.
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Protein Sci,
19,
99.
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R.Torres Martin de Rosales,
M.Faiella,
E.Farquhar,
L.Que,
C.Andreozzi,
V.Pavone,
O.Maglio,
F.Nastri,
and
A.Lombardi
(2010).
Spectroscopic and metal-binding properties of DF3: an artificial protein able to accommodate different metal ions.
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J Biol Inorg Chem,
15,
717-728.
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S.L.Byrne,
N.D.Chasteen,
A.N.Steere,
and
A.B.Mason
(2010).
The unique kinetics of iron release from transferrin: the role of receptor, lobe-lobe interactions, and salt at endosomal pH.
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J Mol Biol,
396,
130-140.
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A.B.Mason,
P.J.Halbrooks,
N.G.James,
S.L.Byrne,
J.K.Grady,
N.D.Chasteen,
C.E.Bobst,
I.A.Kaltashov,
V.C.Smith,
R.T.MacGillivray,
and
S.J.Everse
(2009).
Structural and functional consequences of the substitution of glycine 65 with arginine in the N-lobe of human transferrin.
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Biochemistry,
48,
1945-1953.
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PDB code:
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C.E.Bobst,
M.Zhang,
and
I.A.Kaltashov
(2009).
Existence of a noncanonical state of iron-bound transferrin at endosomal pH revealed by hydrogen exchange and mass spectrometry.
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J Mol Biol,
388,
954-967.
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D.J.Yoon,
D.S.Chu,
C.W.Ng,
E.A.Pham,
A.B.Mason,
D.M.Hudson,
V.C.Smith,
R.T.MacGillivray,
and
D.T.Kamei
(2009).
Genetically engineering transferrin to improve its in vitro ability to deliver cytotoxins.
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J Control Release,
133,
178-184.
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N.G.James,
S.L.Byrne,
A.N.Steere,
V.C.Smith,
R.T.MacGillivray,
and
A.B.Mason
(2009).
Inequivalent contribution of the five tryptophan residues in the C-lobe of human serum transferrin to the fluorescence increase when iron is released.
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Biochemistry,
48,
2858-2867.
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S.Yang,
S.Park,
L.Makowski,
and
B.Roux
(2009).
A rapid coarse residue-based computational method for x-ray solution scattering characterization of protein folds and multiple conformational states of large protein complexes.
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Biophys J,
96,
4449-4463.
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A.B.Mason,
G.L.Judson,
M.C.Bravo,
A.Edelstein,
S.L.Byrne,
N.G.James,
E.D.Roush,
C.A.Fierke,
C.E.Bobst,
I.A.Kaltashov,
and
M.A.Daughtery
(2008).
Evolution reversed: the ability to bind iron restored to the N-lobe of the murine inhibitor of carbonic anhydrase by strategic mutagenesis.
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Biochemistry,
47,
9847-9855.
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A.Yersin,
T.Osada,
and
A.Ikai
(2008).
Exploring transferrin-receptor interactions at the single-molecule level.
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Biophys J,
94,
230-240.
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K.D.Weaver,
J.J.Heymann,
A.Mehta,
P.L.Roulhac,
D.S.Anderson,
A.J.Nowalk,
P.Adhikari,
T.A.Mietzner,
M.C.Fitzgerald,
and
A.L.Crumbliss
(2008).
Ga3+ as a mechanistic probe in Fe3+ transport: characterization of Ga3+ interaction with FbpA.
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J Biol Inorg Chem,
13,
887-898.
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L.F.Murga,
M.J.Ondrechen,
and
D.Ringe
(2008).
Prediction of interaction sites from apo 3D structures when the holo conformation is different.
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Proteins,
72,
980-992.
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Y.Perera,
D.García,
O.Guirola,
V.Huerta,
Y.García,
and
Y.Muñoz
(2008).
Epitope mapping of anti-human transferrin monoclonal antibodies: potential uses for transferrin-transferrin receptor interaction studies.
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J Mol Recognit,
21,
103-113.
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F.S.Domingues,
J.Rahnenführer,
and
T.Lengauer
(2007).
Conformational analysis of alternative protein structures.
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Bioinformatics,
23,
3131-3138.
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H.M.Baker,
D.Nurizzo,
A.B.Mason,
and
E.N.Baker
(2007).
Structures of two mutants that probe the role in iron release of the dilysine pair in the N-lobe of human transferrin.
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Acta Crystallogr D Biol Crystallogr,
63,
408-414.
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PDB codes:
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J.Wally,
and
S.K.Buchanan
(2007).
A structural comparison of human serum transferrin and human lactoferrin.
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Biometals,
20,
249-262.
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A.R.Chaudhuri,
E.M.de Waal,
A.Pierce,
H.Van Remmen,
W.F.Ward,
and
A.Richardson
(2006).
Detection of protein carbonyls in aging liver tissue: A fluorescence-based proteomic approach.
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Mech Ageing Dev,
127,
849-861.
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J.Wally,
P.J.Halbrooks,
C.Vonrhein,
M.A.Rould,
S.J.Everse,
A.B.Mason,
and
S.K.Buchanan
(2006).
The crystal structure of iron-free human serum transferrin provides insight into inter-lobe communication and receptor binding.
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J Biol Chem,
281,
24934-24944.
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PDB codes:
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K.Dassler,
M.Zydek,
K.Wandzik,
M.Kaup,
and
H.Fuchs
(2006).
Release of the soluble transferrin receptor is directly regulated by binding of its ligand ferritransferrin.
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J Biol Chem,
281,
3297-3304.
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A.M.Giannetti,
P.J.Halbrooks,
A.B.Mason,
T.M.Vogt,
C.A.Enns,
and
P.J.Björkman
(2005).
The molecular mechanism for receptor-stimulated iron release from the plasma iron transport protein transferrin.
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Structure,
13,
1613-1623.
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I.Khalaila,
C.S.Allardyce,
C.S.Verma,
and
P.J.Dyson
(2005).
A mass spectrometric and molecular modelling study of cisplatin binding to transferrin.
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Chembiochem,
6,
1788-1795.
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P.T.Gomme,
K.B.McCann,
and
J.Bertolini
(2005).
Transferrin: structure, function and potential therapeutic actions.
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Drug Discov Today,
10,
267-273.
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S.A.Tom-Yew,
D.T.Cui,
E.G.Bekker,
and
M.E.Murphy
(2005).
Anion-independent iron coordination by the Campylobacter jejuni ferric binding protein.
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J Biol Chem,
280,
9283-9290.
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PDB codes:
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D.H.Hamilton,
I.Turcot,
A.Stintzi,
and
K.N.Raymond
(2004).
Large cooperativity in the removal of iron from transferrin at physiological temperature and chloride ion concentration.
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J Biol Inorg Chem,
9,
936-944.
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E.A.Amin,
W.R.Harris,
and
W.J.Welsh
(2004).
Identification of possible kinetically significant anion-binding sites in human serum transferrin using molecular modeling strategies.
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Biopolymers,
73,
205-215.
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Y.Cheng,
O.Zak,
P.Aisen,
S.C.Harrison,
and
T.Walz
(2004).
Structure of the human transferrin receptor-transferrin complex.
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Cell,
116,
565-576.
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PDB code:
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A.Widera,
F.Norouziyan,
and
W.C.Shen
(2003).
Mechanisms of TfR-mediated transcytosis and sorting in epithelial cells and applications toward drug delivery.
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Adv Drug Deliv Rev,
55,
1439-1466.
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D.Rinaldo,
and
M.J.Field
(2003).
A computational study of the open and closed forms of the N-lobe human serum transferrin apoprotein.
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Biophys J,
85,
3485-3501.
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H.M.Baker,
B.F.Anderson,
and
E.N.Baker
(2003).
Dealing with iron: common structural principles in proteins that transport iron and heme.
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Proc Natl Acad Sci U S A,
100,
3579-3583.
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M.Guo,
I.Harvey,
W.Yang,
L.Coghill,
D.J.Campopiano,
J.A.Parkinson,
R.T.MacGillivray,
W.R.Harris,
and
P.J.Sadler
(2003).
Synergistic anion and metal binding to the ferric ion-binding protein from Neisseria gonorrhoeae.
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J Biol Chem,
278,
2490-2502.
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P.Guha Thakurta,
D.Choudhury,
R.Dasgupta,
and
J.K.Dattagupta
(2003).
Structure of diferric hen serum transferrin at 2.8 A resolution.
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Acta Crystallogr D Biol Crystallogr,
59,
1773-1781.
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PDB code:
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S.Dhungana,
C.H.Taboy,
D.S.Anderson,
K.G.Vaughan,
P.Aisen,
T.A.Mietzner,
and
A.L.Crumbliss
(2003).
The influence of the synergistic anion on iron chelation by ferric binding protein, a bacterial transferrin.
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| |
Proc Natl Acad Sci U S A,
100,
3659-3664.
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S.R.Shouldice,
D.R.Dougan,
P.A.Williams,
R.J.Skene,
G.Snell,
D.Scheibe,
S.Kirby,
D.J.Hosfield,
D.E.McRee,
A.B.Schryvers,
and
L.W.Tari
(2003).
Crystal structure of Pasteurella haemolytica ferric ion-binding protein A reveals a novel class of bacterial iron-binding proteins.
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| |
J Biol Chem,
278,
41093-41098.
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PDB code:
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T.E.Adams,
A.B.Mason,
Q.Y.He,
P.J.Halbrooks,
S.K.Briggs,
V.C.Smith,
R.T.MacGillivray,
and
S.J.Everse
(2003).
The position of arginine 124 controls the rate of iron release from the N-lobe of human serum transferrin. A structural study.
|
| |
J Biol Chem,
278,
6027-6033.
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PDB codes:
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U.Nemish,
R.H.Yu,
L.W.Tari,
K.Krewulak,
and
A.B.Schryvers
(2003).
The bacterial receptor protein, transferrin-binding protein B, does not independently facilitate the release of metal ion from human transferrin.
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Biochem Cell Biol,
81,
275-283.
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D.R.Hall,
J.M.Hadden,
G.A.Leonard,
S.Bailey,
M.Neu,
M.Winn,
and
P.F.Lindley
(2002).
The crystal and molecular structures of diferric porcine and rabbit serum transferrins at resolutions of 2.15 and 2.60 A, respectively.
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Acta Crystallogr D Biol Crystallogr,
58,
70-80.
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PDB codes:
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E.N.Baker,
H.M.Baker,
and
R.D.Kidd
(2002).
Lactoferrin and transferrin: functional variations on a common structural framework.
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Biochem Cell Biol,
80,
27-34.
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G.B.Jameson,
B.F.Anderson,
W.A.Breyer,
C.L.Day,
J.W.Tweedie,
and
E.N.Baker
(2002).
Structure of a domain-opened mutant (R121D) of the human lactoferrin N-lobe refined from a merohedrally twinned crystal form.
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Acta Crystallogr D Biol Crystallogr,
58,
955-962.
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PDB code:
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O.Zak,
K.Ikuta,
and
P.Aisen
(2002).
The synergistic anion-binding sites of human transferrin: chemical and physiological effects of site-directed mutagenesis.
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| |
Biochemistry,
41,
7416-7423.
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X.L.Du,
T.L.Zhang,
L.Yuan,
Y.Y.Zhao,
R.C.Li,
K.Wang,
S.C.Yan,
L.Zhang,
H.Sun,
and
Z.M.Qian
(2002).
Complexation of ytterbium to human transferrin and its uptake by K562 cells.
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| |
Eur J Biochem,
269,
6082-6090.
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D.Krzyzanowska,
A.Ozyhar,
A.Lalik,
J.M.Parkitna,
J.Szkudlarek,
K.Waśniowska,
E.Lisowska,
and
M.Kochman
(2001).
Juvenile hormone binding protein and transferrin from Galleria mellonella share a similar structural motif.
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| |
Biol Chem,
382,
1027-1037.
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D.Nurizzo,
H.M.Baker,
Q.Y.He,
R.T.MacGillivray,
A.B.Mason,
R.C.Woodworth,
and
E.N.Baker
(2001).
Crystal structures and iron release properties of mutants (K206A and K296A) that abolish the dilysine interaction in the N-lobe of human transferrin.
|
| |
Biochemistry,
40,
1616-1623.
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PDB codes:
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|
A.H.Yang,
R.T.MacGillivray,
J.Chen,
Y.Luo,
Y.Wang,
G.D.Brayer,
A.B.Mason,
R.C.Woodworth,
and
M.E.Murphy
(2000).
Crystal structures of two mutants (K206Q, H207E) of the N-lobe of human transferrin with increased affinity for iron.
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| |
Protein Sci,
9,
49-52.
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PDB codes:
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K.Mizutani,
H.Yamashita,
B.Mikami,
and
M.Hirose
(2000).
Crystal structure at 1.9 A resolution of the apoovotransferrin N-lobe bound by sulfate anions: implications for the domain opening and iron release mechanism.
|
| |
Biochemistry,
39,
3258-3265.
|
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|
M.Guo,
H.Sun,
H.J.McArdle,
L.Gambling,
and
P.J.Sadler
(2000).
Ti(IV) uptake and release by human serum transferrin and recognition of Ti(IV)-transferrin by cancer cells: understanding the mechanism of action of the anticancer drug titanocene dichloride.
|
| |
Biochemistry,
39,
10023-10033.
|
|
|
|
|
|
|
M.Hirose
(2000).
The structural mechanism for iron uptake and release by transferrins.
|
| |
Biosci Biotechnol Biochem,
64,
1328-1336.
|
|
|
|
|
|
|
N.A.Peterson,
B.F.Anderson,
G.B.Jameson,
J.W.Tweedie,
and
E.N.Baker
(2000).
Crystal structure and iron-binding properties of the R210K mutant of the N-lobe of human lactoferrin: implications for iron release from transferrins.
|
| |
Biochemistry,
39,
6625-6633.
|
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|
PDB code:
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|
Q.Y.He,
A.B.Mason,
R.Pakdaman,
N.D.Chasteen,
B.K.Dixon,
B.M.Tam,
V.Nguyen,
R.T.MacGillivray,
and
R.C.Woodworth
(2000).
Mutations at the histidine 249 ligand profoundly alter the spectral and iron-binding properties of human serum transferrin N-lobe.
|
| |
Biochemistry,
39,
1205-1210.
|
|
|
|
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|
|
R.T.MacGillivray,
M.C.Bewley,
C.A.Smith,
Q.Y.He,
A.B.Mason,
R.C.Woodworth,
and
E.N.Baker
(2000).
Mutation of the iron ligand His 249 to Glu in the N-lobe of human transferrin abolishes the dilysine "trigger" but does not significantly affect iron release.
|
| |
Biochemistry,
39,
1211-1216.
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|
PDB code:
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|
F.B.Abdallah,
and
J.M.Chahine
(1999).
Transferrins, the mechanism of iron release by ovotransferrin.
|
| |
Eur J Biochem,
263,
912-920.
|
|
|
|
|
|
|
H.Kurokawa,
J.C.Dewan,
B.Mikami,
J.C.Sacchettini,
and
M.Hirose
(1999).
Crystal structure of hen apo-ovotransferrin. Both lobes adopt an open conformation upon loss of iron.
|
| |
J Biol Chem,
274,
28445-28452.
|
|
|
PDB code:
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|
K.Mizutani,
H.Yamashita,
H.Kurokawa,
B.Mikami,
and
M.Hirose
(1999).
Alternative structural state of transferrin. The crystallographic analysis of iron-loaded but domain-opened ovotransferrin N-lobe.
|
| |
J Biol Chem,
274,
10190-10194.
|
|
|
PDB codes:
|
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|
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|
|
M.C.Bewley,
B.M.Tam,
J.Grewal,
S.He,
S.Shewry,
M.E.Murphy,
A.B.Mason,
R.C.Woodworth,
E.N.Baker,
and
R.T.MacGillivray
(1999).
X-ray crystallography and mass spectroscopy reveal that the N-lobe of human transferrin expressed in Pichia pastoris is folded correctly but is glycosylated on serine-32.
|
| |
Biochemistry,
38,
2535-2541.
|
|
|
PDB code:
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M.D.Retzer,
R.H.Yu,
and
A.B.Schryvers
(1999).
Identification of sequences in human transferrin that bind to the bacterial receptor protein, transferrin-binding protein B.
|
| |
Mol Microbiol,
32,
111-121.
|
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|
|
P.D.Jeffrey,
M.C.Bewley,
R.T.MacGillivray,
A.B.Mason,
R.C.Woodworth,
and
E.N.Baker
(1998).
Ligand-induced conformational change in transferrins: crystal structure of the open form of the N-terminal half-molecule of human transferrin.
|
| |
Biochemistry,
37,
13978-13986.
|
|
|
PDB codes:
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Y.Li,
W.R.Harris,
A.Maxwell,
R.T.MacGillivray,
and
T.Brown
(1998).
Kinetic studies on the removal of iron and aluminum from recombinant and site-directed mutant N-lobe half transferrins.
|
| |
Biochemistry,
37,
14157-14166.
|
|
|
|
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
