Protoglobin: Structure and Ligand-Binding Properties - Advances in Microbial Physiology - page 81

Sixteen Pgbs have been identified to date in Archaea (five Pgbs) and Bac-
teria ( Hoogewijs, Dewilde, Vierstraete, Moens, & Vinogradov, 2012 ).
Although the physiological role of Pgb is totally unknown, as is the nature
of its physiological ligand(s), over the past few years several progresses have
been made in the structural, biochemical and biophysical characterisation of
this unusual globin, which are reviewed in the following sections.

2. OVERALL STRUCTURE

To date only one Pgb three-dimensional structure, from
M . acetivorans , has been reported ( Nardini et al., 2008 ). The protein bears
the Cys(101)E20

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Ser mutation that was engineered for crystallisation pur-
poses, and hereafter will be simply termed Ma Pgb * .
Ma Pgb * is folded as an expanded version of the canonical globin fold (i.e.
the Mb fold), consisting of a 3-on-3 a -helical sandwich built by the AGH-
BEF helices, with the support of the C- and D-helices ( Bolognesi et al.,
1997; Perutz, 1979 ). Contrary to the classical globin fold, however, in
Ma Pgb * , the D-helix is absent, an additional N-terminal Z-helix precedes
the A-helix, and a short H 0 -helix (one helical turn) falls close to the
C-terminus. The Z-helix is further preceded by 20 amino acids held next
to the haem propionates by hydrogen bonds that link Pro(7), Gly(8),
Tyr(9), Thr(10), Ala(18) and Phe(20) to residues of the E- and F-helices
in the protein a -helical core. As a consequence, this N-terminal loop
together with other extended loops connecting the C-helix with the
E-helix and the F-helix with the G-helix (which all are longer than in clas-
sical globins and are conserved in known Pgb amino acid sequences)
completely bury the haem within the protein matrix, and the haem propi-
onates are solvent inaccessible ( Fig. 3.1 A). Such structural feature is very
unusual within the globin family 3D structures, where approximately
30% of the haem surface is usually solvent accessible. Thus, ligand diffusion
to the haem pocket in Ma Pgb * must occur via paths different from direct
haem access through the E7 residue gate. The proposed alternative ligand dif-
fusion paths in Ma Pgb * are located between the B- and G-helices (tunnel 1),
and between the B- and E-helices (tunnel 2) ( Fig. 3.1 B).
The location and extention of the Z-helix in the Pgb fold are reminiscent
of the globin domain of the haem-based O 2 sensor responsible for aerotaxis
in aerobic Bacillus subtilis ( Zhang & Phillips, 2003 ), and of the GCS globin
domain from the strictly anaerobic d -proteobacterium Geobacter
sulfurreducens ( Pesce et al., 2009 ), with which Ma Pgb * shares approximately