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PDBsum entry 2j0r
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Transport protein
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PDB id
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2j0r
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References listed in PDB file
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Key reference
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Title
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An induced fit conformational change underlies the binding mechanism of the heme transport proteobacteria-Protein hems.
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Authors
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S.Schneider,
K.H.Sharp,
P.D.Barker,
M.Paoli.
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Ref.
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J Biol Chem, 2006,
281,
32606-32610.
[DOI no: ]
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PubMed id
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Abstract
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Bacteria rely on their environment and/or host to acquire iron and have evolved
specialized systems to sequester and transport heme. The heme uptake system
HemRSTUV is common to proteobacteria, and a major challenge is to understand the
molecular mechanism of heme binding and transfer between the protein molecules
that underlie this heme transport relay process. In the Gram-negative pathogen
Yersinia enterocolitica, the HemRSTUV system culminates with the cytoplasmic
recipient HemS, which stores and delivers heme for cellular needs. HemS belongs
to a family of proteins essential and unique to proteobacteria. Here we report
on the binding mechanism of HemS based on structural data from its apo- and
ligand-loaded forms. This heme carrier protein associates with its cargo through
a novel, partly preformed binding pocket, formed between a large beta-sheet dome
and a three-helix subdomain. In addition to a histidine interacting with the
iron, the complex is stabilized by a distal non-coordinating arginine that packs
along the porphyrin plane and extensive electrostatic contacts that firmly
anchor the heme propionate groups within the protein. Comparison of apo- and
ligand-bound HemS crystal structures reveals striking conformational changes
that underlie a "heme-induced fit" binding mechanism. Local shifts in
amino acid positions combine with global, rigid body-like domain movements, and
together, these bring about a switch from an open, apo-form to a closed, bound
state. This is the first report in which both liganded and unliganded forms of a
heme transport protein are described, thus providing penetrating insights into
its mechanism of heme binding and release.
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Figure 2.
FIGURE 2. Heme-protein interactions. A, heme-binding pocket
in the heme-HemS complex. Residues provided by the N-terminal
domain are colored in blue, and residues provided by the
C-terminal domain are in red. His-196 stems from the beginning
of helix  7 and coordinates the
iron. Arg-102 extends over the porphyrin plane next to Leu-94.
B, residues interacting with the heme propionates. An extensive
electrostatic/polar network of seven direct and two
water-mediated (not shown) contacts firmly anchor the propionate
groups.
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Figure 4.
FIGURE 4. The HemS conformational switch between apo, open
state and liganded, closed state. The superposition was prepared
as in Fig. 3. The heme complex is shown in green, and the
apo-structure is shown in gold. The superposition shows the
global interdomain movements in HemS that effectively clamp the
ligand in the binding site. N-domain, N-terminal domain;
C-domain, C-terminal domain.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2006,
281,
32606-32610)
copyright 2006.
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Secondary reference #1
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Title
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Crystallization and preliminary X-Ray diffraction analysis of the haem-Binding protein hems from yersinia enterocolitica.
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Authors
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S.Schneider,
M.Paoli.
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Ref.
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Acta Crystallogr Sect F Struct Biol Cryst Commun, 2005,
61,
802-805.
[DOI no: ]
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PubMed id
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Figure 2.
Crystallization of HemS from Y. enterocolitica. (a) Needle
clusters observed in the 'hit' condition identified from the
high-throughput screening of 864 conditions in sitting-drop
vapour-diffusion experiments: 0.1 M MES, 2.0 M ammonium sulfate,
5% PEG 400 pH 6.5. (b) Improved conditions in hanging drops: 0.1
M MES pH 6.5, 1.8 M ammonium sulfate and 4% PEG 400. (c) and (d)
Crystals obtained through further optimization in hanging drops
in 0.1 M Tris --HCl pH 8.5, 1.8 M ammonium sulfate, 2% PEG 400;
drop size was 2 + 2 [micro]l and protein concentration 30 mg
ml^[minus sign]1 (bar indicates 100 [micro]m). Acta Crystallogr
Sect F Struct Biol Cryst Commun. 2005 August 1; 61(Pt 8):
802–805. Published online 2005 July 30. doi:
10.1107/S1744309105023523. Copyright [copyright] International
Union of Crystallography 2005
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Figure 3.
Image showing a typical diffraction pattern from HemS
crystals obtained using the laboratory radiation source. The
figure was produced with MOSFLM (Leslie, 1992[triangle]). Acta
Crystallogr Sect F Struct Biol Cryst Commun. 2005 August 1;
61(Pt 8): 802–805. Published online 2005 July 30. doi:
10.1107/S1744309105023523. Copyright [copyright] International
Union of Crystallography 2005
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The above figures are
reproduced from the cited reference
which is an Open Access publication published by the IUCr
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