4YEH

Crystal structure of Mg2+ ion containing hemopexin fold from Kabuli chana (chickpea white) at 2.45A resolution reveals a structural basis of metal ion transport

Summary for 4YEH

• Entry DOI: 10.2210/pdb4yeh/pdb
• Descriptor: Lectin, MAGNESIUM ION (3 entities in total)
• Functional Keywords: plant protein
• Biological source: Cicer arietinum (Chickpea)
• Total number of polymer chains: 2
• Total formula weight: 50843.92

Authors

Kumar, S.,Singh, A.,Yamini, S.,Bhushan, A.,Dey, S.,Sharma, S.,Singh, T.P. (deposition date: 2015-02-24, release date: 2015-03-25, Last modification date: 2023-11-08)

Primary citation

Kumar, S.,Singh, A.,Yamini, S.,Dey, S.,Singh, T.P.
Crystal Structure of Mg(2+) Containing Hemopexin-Fold Protein from Kabuli Chana (Chickpea-White, CW-25) at 2.45 angstrom Resolution Reveals Its Metal Ion Transport Property
Protein J., 34:284-290, 2015

PubMed Abstract: 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.

PubMed: 26242869
DOI: 10.1007/s10930-015-9624-z

Experimental method

X-RAY DIFFRACTION (2.45 Å)