Structure of Ferric Soybean LeghemoglobinaNicotinate at 2.3 Å Resolution

Abstract

Soybean leghemoglobin a is a small (16 kDa) protein facilitating the transport of Oz to respiring N2-fixing bacteria at low free-O2 tension. The crystal structure of soybean ferric leghemoglobin a nicotinate has been refined at 2.3 A resolution. The final R factor is 15.8% for 6877 reflections between 6.0 and 2.3 ~. The structure of soybean leghemoglobin a (143 residues) is closely similar to that of lupin leghemoglobin II (153 residues), the proteins having 82 identical residues when the sequences are aligned. The new structure provides support for the conclusion that the unique properties of leghemoglobin arise principally from a heme pocket considerably larger and more flexible than that of myoglobin, a strongly ruffled heme group, and a proximal histidine orientation more favourable to ligand binding.

Characterization of Determinants of Ligand Binding to the Nicotinic Acid Receptor GPR109A (HM74A/PUMA-G)

“…According to several X-ray structures of nicotinic acid/ protein complexes, in which nicotinic acid is surrounded by aromatic residues (Reddy et al, 1996;Ellis et al, 1997;Cheong et al, 1999Cheong et al, , 2001Lovering et al, 2001), and based on our docking model of nicotinic acid/GPR109A, the participation of aromatic residues as direct and indirect partners in the binding site was predicted. To distinguish between direct and indirect aromatic interaction partners of the ligand, we introduced strong (alanine) and weak (leucine) alterations of side-chain properties by mutations.…”

“…From analyses of crystal structures of nicotinic acid bound at diverse prokaryotic proteins [such as nicotinate mononucleotide dimethylbenzimidazole phosphoribosyltransferase (PDB code 1D0V) (Cheong et al, 1999), dihydropteridine reductase (PDB code 1ICR) (Lovering et al, 2001), nicotinate nucleotide dimethylbenzimidazole phosphoribosyltransferase (PDB code 1JHA) (Cheong et al, 2001), dihydrodipicolinate reductase (PDB code 1DRV) (Reddy et al, 1996), and the plant protein ferric soybean leghemoglobin (PDB code 1FSL) (Ellis et al, 1997)], it is evident that the pyridine ring system of the ligand is always bound near aromatic side chains of the protein. Following the structural homology paradigm, we assumed that the binding pocket of GPR109A is also coated by aromatic side chain(s) as an additional binding partner for nicotinic acid.…”

Designer haem proteins: What can we learn from protein engineering?

“…A crystal structure for the leghemoglobin a from soybean is shown in Fig. 6 [22,23]. We have reported [24] the generation of a synthetic gene for soybean Lba and have established that the recombinant protein derived from expression of this gene in Escherishcia coli is an authentic duplicate of the wild-type soybean Lba.…”

Modeling the tertiary structure of a maize (Zea mays ssp. mays) non-symbiotic hemoglobin

“…The resulting Lba model was compared with the Lba tertiary structure [12,17] deposited in the Brookhaven Protein Data Base (http://www.rcsb.org/pdb) under the accession number 1FSL.…”