Nitrobindin: An Ubiquitous Family of All β‐Barrel Heme‐proteins

Abstract

Rhodnius prolixus nitrophorins (Rp-NPs), Arabidopsis thaliana nitrobindin (At-Nb), and Homo sapiens THAP4 (Hs-THAP4) are the unique known proteins that use a b-barrel fold to bind ferric heme, which is devoted to NO transport and/or catalysis. The eight-stranded antiparallel b-barrel Rp-NPs, which represent the only heme-binding lipocalins, are devoted to deliver NO into the blood vessel of the host and to scavenge histamine during blood sucking. Regarding Nbs, crystallographic data suggest the ability of At-Nb and Hs-THAP4 to bind ferric heme; however, no data are available with respect to these functions in the natural host. Here, a bioinformatics investigation based on the amino acid sequences and threedimensional structures of At-Nb and Hs-THAP4 suggests a conservation of the 10-stranded antiparallel b-barrel Nb structural module in all life kingdoms of the evolutionary ladder. In particular, amino acid residues involved in the heme recognition and in the structure stabilization of the Nb structural module are highly conserved (identity > 29%; homology > 83%). Moreover, molecular models of putative Nbs from different organisms match very well with each other and known threedimensional structures of Nbs. Furthermore, phylogenetic tree reconstruction indicates that NPs and Nbs group in distinct clades. These data indicate that 10-stranded b-barrel Nbs constitute a new ubiquitous heme protein family spanning from bacteria to Homo sapiens. V C 2016 IUBMB Life, 68(6): [423][424][425][426][427][428] 2016

Rational design of metalloenzymes: From single to multiple active sites

“…Therefore, it is of importance to employ the cavity of other proteins with a larger volume for design of metalloenzymes with advanced functions. Nitrobindin (NB) is a rigid β-barrel protein with a large hydrophobic pocket harboring a heme for NO transport in vivo [147], which retains the unique structure in its apo-form by removal of heme, and is thus favorable for incorporation of other metal complexes.…”

Artificial Enzymes for Diels‐Alder Reactions

“…NBs belong to an ubiquitous family of all β-barrel proteins that display hydrophobic cavities containing a labile native heme cofactor. [111] Several NB variants were prepared. All of them contained a cysteine residue in position 96 (C96, Figure 18).…”

Nitrophorins and nitrobindins: structure and function

“…Although Nbs have been identified in different species and show a 'FABP-like' ten-stranded β-barrel fold, they (i) possess cross-barrel electrostatic interactions that are absent in FABPs and (ii) do not show the two α-helices followed by a hairpin on the opposite side of the barrel that are present in FABPs (33). Moreover, the phylogenetic tree reconstruction indicates that Nbs and FABPs cluster separately, Nbs forming a ubiquitous heme-protein family spanning from bacteria to Hs (33). All the Nb-like proteins display conserved residues in the pocket involved in the coordination and recognition of the heme-Fe.…”

“…The N-terminal 3 10 helix of At-Nb closes the hydrophobic core of the protein and is stabilized by hydrogen bonds between the Trp30 side chain and the backbone carbonyl group of the Leu26 residue and between the Lys165 side chain and the carbonyl groups of Tyr25 and Leu27 residues (33). The central part of the β-barrel of At-Nb is stabilized by two salt bridges between Arg133 and the carboxylate groups of Glu78 and Glu102 and by two strong hydrogen bonds between Tyr144 and Glu48 and between Glu78 and Tyr62 (33) ( Figure 5).…”

“…ligand transport, storage and sensing) similar to those of all α-helical globins. They include Rhodnius prolixus nitrophorins (Rp-NPs) (25)(26)(27), human α 1 -microglobulin (Hs-α 1 -m) (28,29), Cimex lectularius nitrophorin (Cl-NP) (30), Arabidopsis thaliana nitrobindin (At-Nb) and Homo sapiens THAP4 (Hs-THAP4) (31)(32)(33).…”