Crystal structure of narbonin at 1.8 Å resolution

Abstract

The three-dimensional structure of narbonin, a seed protein from Vicia narbonensis L, has been determined at 1.8 A resolution. Phase information was obtained by multiple isomorphous replacement and optimized anomalous dispersion. The narbonin structure was initially traced with only 17% amino-acid sequence information and preliminarily refined to a crystallographic R-factor of 16.5%. It is now refined to 15.9% using full sequence information derived from cDNA and after the addition of more solvent molecules. The monomeric molecule of narbonin is an eight-stranded parallel beta-barrel surrounded by alpha-helices in a beta/alpha-topology similar to that first observed in triose phosphate isomerase. Differences exist in the N-terminal part of the polypeptide chain, where the first helix is replaced by a loop and the second beta-strand is followed by an additional antiparallel alpha-sheet placed parallel on top of alpha-helices alpha3 and alpha4. Two short additional secondary structures are present. The first, an alpha-helix, is situated between the seventh beta-strand and the following helix, and the second, which is a 3(10) helix, between the eighth strand and the C-terminal helix. The most striking observation is the lack of a known enzymatic function for narbonin, because all TIM-like structures known so far are enzymes.

The 1.8 Å Resolution Structure of Hevamine, a Plant Chitinase/Lysozyme, and Analysis of the Conserved Sequence and Structure Motifs of Glycosyl Hydrolase Family 18

“…The structures of concanavalin B (Hennig et al, 1995a; PDB entry 1CNV), narbonin (Hennig et al, 1995b; PDB entry 1NAR), chitinase A (Perrakis et al, 1994;PDB entry 1CTN), endo F1 (van Roey et al, 1994; PDB entry 2EBN), endo H (Rao et al, 1995;PDB entry 1EDT) and the a-subunit of tryptophan synthase (Hyde et al, 1988; PDB entry 1WSY) were superimposed on the hevamine model using the option of the program O (Jones et al, 1991) to locate the longest matching fragments between two molecules, where each pair of C a atoms in a fragment should fit better than 3.8 Å . The assignment of equivalent C a pairs was checked and improved by hand, using the information of the sumperimposed three-dimensional structures.…”

“…Five other proteins with known X-ray structures contain the family 18 consensus regions, being chitinase A from Serratia marcescens (Perrakis et al, 1994), endo-b-N-acetylglucosaminidase F 1 (endo F 1 ) from Flavobacterium meningosepticum (van Roey et al, 1994), endo-b-N-acetylglucosaminidase H (endo H) from Streptomyces plicatus (Rao et al, 1995), and the plant proteins concanavalin B from Canavalia ensiformis (Hennig et al, 1995a) and narbonin from Vicia narbonensis (Hennig et al, 1995b). Endo F 1 and endo H cleave the b(1,4)-glycosidic bond between the two core N-acetylglucosamine residues of asparagine-linked oligosaccharides, for narbonin and concanavalin B no enzymatic activity is known.…”

Structural Investigation of a Novel N-Acetyl Glucosamine Binding Chi-Lectin Which Reveals Evolutionary Relationship with Class III Chitinases

“…Narbonin from the seeds of Vicia narbonensis and Vicia pannonica is also reported as a member of this family that lacks chitinase activity [49], [50], [51]. Narbonin has Glu132 at similar position to hevamine catalytic glutamate and still do not show chitinase activity as Glu132 is engaged with Arg87 in forming salt bridge.…”

Crystal structure of class III chitinase from pomegranate provides the insight into its metal storage capacity

“…5) More recently, they are further divided into seven classes, I-VII. 6) In general, class I and II chitinases possess GH-19 catalytic domain and α + β structure, whereas class III chitinase has GH-18 catalytic domain with (β/α) 8 barrel folding. Judging from the primary structure, the plant class III chitinase shares some common characteristics, i.e.…”

“…it possesses catalytic "DXDXE motif" in its sequence, conserved three disulfide bonds, and the folding rather similar to that of bacterial and fungal chitinases, in spite of poor sequence similarity. In addition, there is a protein family homologous to class III chitinase that does not possess the GH enzymatic activity, but functions as a carbohydrate-binding protein (lectin) or seed storage protein, such as concanavarin B, 7) nanovarin, 8) and chitinase like lectin (chi-lectin). 9) These members have similar primary structures and three-dimensional structure (TIM-barrel (β/α) 8 -fold) to that of the plant type III chitinase, 10) although the active site acidic residues are substituted.…”