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PDBsum entry 4jhh
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Plant protein
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PDB id
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4jhh
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References listed in PDB file
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Key reference
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Title
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The landscape of cytokinin binding by a plant nodulin.
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Authors
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M.Ruszkowski,
K.Szpotkowski,
M.Sikorski,
M.Jaskolski.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2013,
69,
2365-2380.
[DOI no: ]
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PubMed id
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Abstract
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Nodulation is an extraordinary symbiotic interaction between leguminous plants
and nitrogen-fixing bacteria (rhizobia) that assimilate atmospheric nitrogen (in
root nodules) and convert it into compounds suitable for the plant host. A class
of plant hormones called cytokinins are involved in the nodulation process. In
the model legume Medicago truncatula, nodulin 13 (MtN13), which belongs to the
pathogenesis-related proteins of class 10 (PR-10), is expressed in the outer
cortex of the nodules. In general, PR-10 proteins are small and monomeric and
have a characteristic fold with an internal hydrophobic cavity formed between a
seven-stranded antiparallel β-sheet and a C-terminal α-helix. Previously, some
PR-10 proteins not related to nodulation were found to bind cytokinins such as
trans-zeatin. Here, four crystal structures of the MtN13 protein are reported in
complexes with several cytokinins, namely trans-zeatin, N(6)-isopentenyladenine,
kinetin and N(6)-benzyladenine. All four phytohormones are bound in the
hydrophobic cavity in the same manner and have excellent definition in the
electron-density maps. The binding of the cytokinins appears to be strong and
specific and is reinforced by several hydrogen bonds. Although the binding
stoichiometry is 1:1, the complex is actually dimeric, with a cytokinin molecule
bound in each subunit. The ligand-binding site in each cavity is formed with the
participation of a loop element from the other subunit, which plugs the only
entrance to the cavity. Interestingly, a homodimer of MtN13 is also formed in
solution, as confirmed by small-angle X-ray scattering (SAXS).
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Secondary reference #1
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Title
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Structural and functional aspects of pr-10 proteins.
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Authors
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H.Fernandes,
K.Michalska,
M.Sikorski,
M.Jaskolski.
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Ref.
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Febs J, 2013,
280,
1169-1199.
[DOI no: ]
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PubMed id
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Secondary reference #2
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Title
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Lupinus luteus pathogenesis-Related protein as a reservoir for cytokinin.
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Authors
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H.Fernandes,
O.Pasternak,
G.Bujacz,
A.Bujacz,
M.M.Sikorski,
M.Jaskolski.
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Ref.
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J Mol Biol, 2008,
378,
1040-1051.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1. Overall fold of the LlPR-10.2B molecule with
annotation of secondary-structure elements. The three
trans-zeatin molecules found inside the binding cavity are shown
in ball-and-stick representation. The binding cavity is
represented as a gray cast, calculated in VOIDOO.^34 A calcium
cation is represented as a sphere. The orientation has been
adjusted to visualize the O16 atoms of the zeatin molecules.
This and all other structural illustrations have been prepared
using PyMol [http://pymol.sourceforge.net/].
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Figure 5.
Fig. 5. Representation of the three zeatin molecules found in
the protein cavity (black outline) with their environment.
Hydrogen bonds are represented by dash lines. Those formed by
the zeatin molecules are annotated with the donor–acceptor
distance in angstroms. The letters a–c mark water molecules
that are linked by hydrogen bonds but could not be connected
because of the distortion of this two-dimensional
representation. The residues involved in hydrogen bonding are
represented in stick mode (gray, if they participate in van der
Waals interactions with the ligands). The ellipses indicate
amino acid residues involved only in van der Waals contacts with
the zeatin molecules. The asterisk * indicates a water molecule
that has hydrogen-bonding interactions with bulk solvent only.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #3
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Title
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Cytokinin-Induced structural adaptability of a lupinus luteus pr-10 protein.
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Authors
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H.Fernandes,
A.Bujacz,
G.Bujacz,
F.Jelen,
M.Jasinski,
P.Kachlicki,
J.Otlewski,
M.M.Sikorski,
M.Jaskolski.
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Ref.
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Febs J, 2009,
276,
1596-1609.
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PubMed id
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Secondary reference #4
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Title
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Crystal structure of vigna radiata cytokinin-Specific binding protein in complex with zeatin.
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Authors
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O.Pasternak,
G.D.Bujacz,
Y.Fujimoto,
Y.Hashimoto,
F.Jelen,
J.Otlewski,
M.M.Sikorski,
M.Jaskolski.
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Ref.
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Plant Cell, 2006,
18,
2622-2634.
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PubMed id
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Secondary reference #5
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Title
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Symbiosis-Specific expression of two medicago truncatula nodulin genes, Mtn1 and mtn13, Encoding products homologous to plant defense proteins.
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Authors
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P.Gamas,
F.De billy,
G.Truchet.
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Ref.
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Mol Plant Microbe Interact, 1998,
11,
393-403.
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PubMed id
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