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PDBsum entry 1yuf
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Growth factor
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PDB id
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1yuf
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Contents |
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* Residue conservation analysis
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DOI no:
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Biochemistry
32:7334-7353
(1993)
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PubMed id:
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Solution structure of human type-alpha transforming growth factor determined by heteronuclear NMR spectroscopy and refined by energy minimization with restraints.
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F.J.Moy,
Y.C.Li,
P.Rauenbuehler,
M.E.Winkler,
H.A.Scheraga,
G.T.Montelione.
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ABSTRACT
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Human type-alpha transforming growth factor (hTGF alpha) is a small mitogenic
protein containing 50 amino acids and 3 disulfide bonds. Homo- and heteronuclear
NMR spectra were used to determine nearly complete sequence-specific 1H and 15N
resonance assignments for hTGF alpha under three conditions: pH 6.5 and a
temperature of 10 degrees C, pH 6.5 and a temperature of 30 degrees C, and pH
3.5 and a temperature of 30 degrees C. The 15N-enriched samples of hTGF alpha
allowed determination of many 3J(HN-H alpha) vicinal coupling constants.
Solution structures of human type-alpha transforming growth factor (hTGF alpha)
at pH 6.5 and a temperature of 10 degrees C were determined from NMR data using
molecular structure generation calculations and restrained energy minimization.
These structures are based on 425 conformational constraints, including 357
NOE-derived upper-bound distance constraints, constraints on the ranges of 26
dihedral angles based on measurements of vicinal coupling constants, 42 upper-
and lower-bound constraints associated with 6 hydrogen bonds and 3 disulfide
bonds, and several stereospecific 1H resonance assignments. The overall
structure is similar to that described recently for hTGF alpha by other groups
[Kline et al. (1990) Biochemistry 29, 7805-7813; Harvey et al. (1991). Eur. J.
Biochem. 198, 555-562], but there are differences in some structural details.
The resonance frequencies, vicinal coupling constants, and NOEs form the basis
for comparisons of the solution structure of hTGF alpha at neutral and acidic
pH. At pH 3.5 the protein structure is partially disordered, with most of the
hydrogen-bonded backbone structure still intact. The hTGF alpha structure is
also compared with that of murine epidermal growth factor. Coordinates for the
set of hTGF alpha structures described in this paper have been deposited in the
Protein Data Bank.
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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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K.Nagata
(2010).
Studies of the structure-activity relationships of peptides and proteins involved in growth and development based on their three-dimensional structures.
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Biosci Biotechnol Biochem,
74,
462-470.
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Q.Guo,
M.Manolopoulou,
Y.Bian,
A.B.Schilling,
and
W.J.Tang
(2010).
Molecular basis for the recognition and cleavages of IGF-II, TGF-alpha, and amylin by human insulin-degrading enzyme.
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J Mol Biol,
395,
430-443.
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PDB codes:
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I.Iloro,
D.Narváez,
N.Guillén,
C.M.Camacho,
L.Guillén,
E.Cora,
and
B.Pastrana-Ríos
(2008).
The kinetics of the hydrogen/deuterium exchange of epidermal growth factor receptor ligands.
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Biophys J,
94,
4041-4055.
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M.Wingens,
T.Walma,
H.van Ingen,
C.Stortelers,
J.E.van Leeuwen,
E.J.van Zoelen,
and
G.W.Vuister
(2003).
Structural analysis of an epidermal growth factor/transforming growth factor-alpha chimera with unique ErbB binding specificity.
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J Biol Chem,
278,
39114-39123.
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PDB code:
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W.Li,
Y.Zhang,
D.Kihara,
Y.J.Huang,
D.Zheng,
G.T.Montelione,
A.Kolinski,
and
J.Skolnick
(2003).
TOUCHSTONEX: protein structure prediction with sparse NMR data.
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Proteins,
53,
290-306.
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T.P.Garrett,
N.M.McKern,
M.Lou,
T.C.Elleman,
T.E.Adams,
G.O.Lovrecz,
H.J.Zhu,
F.Walker,
M.J.Frenkel,
P.A.Hoyne,
R.N.Jorissen,
E.C.Nice,
A.W.Burgess,
and
C.W.Ward
(2002).
Crystal structure of a truncated epidermal growth factor receptor extracellular domain bound to transforming growth factor alpha.
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Cell,
110,
763-773.
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PDB code:
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C.McInnes,
J.Wang,
A.E.Al Moustafa,
C.Yansouni,
M.O'Connor-McCourt,
and
B.D.Sykes
(1998).
Structure-based minimization of transforming growth factor-alpha (TGF-alpha) through NMR analysis of the receptor-bound ligand. Design, solution structure, and activity of TGF-alpha 8-50.
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J Biol Chem,
273,
27357-27363.
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D.Tolkatchev,
and
F.Ni
(1998).
Calcium binding properties of an epidermal growth factor-like domain from human thrombomodulin.
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Biochemistry,
37,
9091-9100.
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C.McInnes,
and
B.D.Sykes
(1997).
Growth factor receptors: structure, mechanism, and drug discovery.
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Biopolymers,
43,
339-366.
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C.E.White,
M.J.Hunter,
D.P.Meininger,
S.Garrod,
and
E.A.Komives
(1996).
The fifth epidermal growth factor-like domain of thrombomodulin does not have an epidermal growth factor-like disulfide bonding pattern.
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Proc Natl Acad Sci U S A,
93,
10177-10182.
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C.McInnes,
D.W.Hoyt,
R.N.Harkins,
R.N.Pagila,
M.T.Debanne,
M.O'Connor-McCourt,
and
B.D.Sykes
(1996).
NMR study of the transforming growth factor-alpha (TGF-alpha)-epidermal growth factor receptor complex. Visualization of human TGF-alpha binding determinants through nuclear Overhauser enhancement analysis.
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J Biol Chem,
271,
32204-32211.
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L.Jendeberg,
M.Tashiro,
R.Tejero,
B.A.Lyons,
M.Uhlén,
G.T.Montelione,
and
B.Nilsson
(1996).
The mechanism of binding staphylococcal protein A to immunoglobin G does not involve helix unwinding.
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Biochemistry,
35,
22-31.
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PDB code:
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N.E.Jacobsen,
N.Abadi,
M.X.Sliwkowski,
D.Reilly,
N.J.Skelton,
and
W.J.Fairbrother
(1996).
High-resolution solution structure of the EGF-like domain of heregulin-alpha.
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Biochemistry,
35,
3402-3417.
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PDB codes:
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R.Tejero,
D.Bassolino-Klimas,
R.E.Bruccoleri,
and
G.T.Montelione
(1996).
Simulated annealing with restrained molecular dynamics using CONGEN: energy refinement of the NMR solution structures of epidermal and type-alpha transforming growth factors.
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Protein Sci,
5,
578-592.
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C.C.Lester,
B.Wang,
R.Wu,
and
H.A.Scheraga
(1995).
Structure-function studies of mEGF: probing the type I beta-turn between residues 25 and 26.
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J Protein Chem,
14,
753-762.
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D.P.Meininger,
M.J.Hunter,
and
E.A.Komives
(1995).
Synthesis, activity, and preliminary structure of the fourth EGF-like domain of thrombomodulin.
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Protein Sci,
4,
1683-1695.
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PDB code:
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M.J.Hunter,
and
E.A.Komives
(1995).
Thrombin-binding affinities of different disulfide-bonded isomers of the fifth EGF-like domain of thrombomodulin.
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Protein Sci,
4,
2129-2137.
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K.Nagata,
D.Kohda,
H.Hatanaka,
S.Ichikawa,
S.Matsuda,
T.Yamamoto,
A.Suzuki,
and
F.Inagaki
(1994).
Solution structure of the epidermal growth factor-like domain of heregulin-alpha, a ligand for p180erbB-4.
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EMBO J,
13,
3517-3523.
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PDB codes:
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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
codes are
shown on the right.
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