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PDBsum entry 4yeh
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Plant protein
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PDB id
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4yeh
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References listed in PDB file
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Key reference
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Title
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Crystal structure of mg(2+) containing hemopexin-Fold protein from kabuli chana (chickpea-White, Cw-25) at 2.45 å resolution reveals its metal ion transport property.
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Authors
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S.Kumar,
A.Singh,
S.Yamini,
S.Dey,
T.P.Singh.
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Ref.
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Protein J, 2015,
34,
284-290.
[DOI no: ]
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PubMed id
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Abstract
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Plant seeds contain a number of proteins which play important roles in the
protection and the process of germination of seeds. We have isolated and
purified a 25 kDa protein from Kabuli Chana (Cicer arietinum L.,
Chickpea-white, CW-25). The CW-25 protein was crystallized using 0.5 M
magnesium acetate, 0.1 M sodium cacodylate and 20 % (w/v) polyethylene glycol
8000, pH 6.5. The crystals of CW-25 belonged to space group P3 with unit cell
dimensions, a = b = 80.5 Å, and c = 69.2 Å. The structure of CW-25 was
determined using molecular replacement method and refined to an R factor of
0.152. The buried surface area between two molecules was found to be
approximately 653 Å(2) indicating the formation of a weak homodimer. The
polypeptide chain of CW-25 adopted a hemopexin-fold with four-bladed
β-propellers. The structure formed a central tunnel-like architecture. A
magnesium ion was observed in the centre of the tunnel. It was located at
distances varying between 2.3 and 2.7 Å from five oxygen atoms of which four
were backbone oxygen atoms belonging to residues, Asn7, Asp65, Asp121 and Asp174
while the fifth oxygen atom, O(δ1) was from the side chain of Asn7. The
approximate length of the tunnel was 30 Å. Furthermore, a series of carbonyl
oxygen atoms were present along the internal face of the tunnel. The diameter of
the tunnel varied from 4.6 to 6.2 Å. The diameter and chemical environment of
the tunnel clearly indicated that it might be used for the transport of various
metal ions across the molecule.
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