The three-dimensional structure of Aspergillus niger pectin lyase B (PLB) has been determined by crystallographic techniques at a resolution of 1.7 A. The model, with all 359 amino acids and 339 water molecules, refines to a final crystallographic R factor of 16.5%. The polypeptide backbone folds into a large right-handed cylinder, termed a parallel beta helix. Loops of various sizes and conformations protrude from the central helix and probably confer function. The largest loop of 53 residues folds into a small domain consisting of three antiparallel beta strands, one turn of an alpha helix, and one turn of a 3(10) helix. By comparison with the structure of Erwinia chrysanthemi pectate lyase C (PelC), the primary sequence alignment between the pectate and pectin lyase subfamilies has been corrected and the active site region for the pectin lyases deduced. The substrate-binding site in PLB is considerably less hydrophilic than the comparable PelC region and consists of an extensive network of highly conserved Trp and His residues. The PLB structure provides an atomic explanation for the lack of a catalytic requirement for Ca2+ in the pectin lyase family, in contrast to that found in the pectate lyase enzymes. Surprisingly, however, the PLB site analogous to the Ca2+ site in PelC is filled with a positive charge provided by a conserved Arg in the pectin lyases. The significance of the finding with regard to the enzymatic mechanism is discussed.
Electron Paramagnetic Resonance (EPR) spectroscopy was used to study Cu(II) dynamic behavior in a doped biological model crystal; bis(L-histidinato)cadmium dihydrate, in order to gain better insight into copper site stability in metalloproteins. Temperature dependent changes in the low temperature X-band EPR spectra became visible around 100 K and continued up to room temperature. The measured 298 K g-tensor (principal values: 2.17, 2.16, 2.07) and copper hyperfine coupling tensor (principal values: −260, − 190, −37 MHz) were similar to the average of the 77 K tensor values pertaining to two neighboring histidine binding sites. The observed temperature dependence was interpreted using Anderson’s theory of motional narrowing, where the magnetic parameters for the different states are averaged as the copper rapidly hops between sites. The EPR pattern was also found to undergo a sharp sigmoidal-shaped, temperature dependent conversion between two species with a critical temperature Tc ≈ 160 K. The species below Tc hops between the two low temperature site patterns, and the one above Tc represents an average of the molecular spin Hamiltonian coupling tensors of the two 77 K sites. In addition, the low and high temperature species hop between one another, contributing to the dynamic averaging. Spectral simulations using this 4-state model determined a hop rate between the two low temperature sites νh4 = 4.5 × 108 s−1 and between the low and high temperature states νh2 = 1.7 × 108 s−1 at 160 K. An Arrhenius relationship of hop rate and temperature gave energy barriers of ΔE4 = 389 cm−1 and ΔE2 = 656 cm−1 between the two low temperature sites, and between the low and high temperature states, respectively.
The parallel beta helix structure found in the pectate lyase superfamily has been analyzed in detail. A comparative analysis of known structures has revealed a unique sequence profile, with a strong positional preference for specific amino acids oriented toward the interior of the parallel beta helix. Using the unique sequence profile, search patterns have been constructed and applied to the sequence databases to identify a subset of proteins that are likely to fold into the parallel beta helix. Of the 19 families identified, 39% are known to be carbohydrate-binding proteins, and 50% belong to a broad category of proteins with sequences containing leucine-rich repeats (LRRs). The most striking result is the sequence match between the search pattern and four contiguous segments of internalin A, a surface protein from the bacterial pathogen Listeria monocytogenes. A plausible model of the repetitive LRR sequences of internalin A has been constructed and favorable 3D-1D profile scores have been calculated. Moreover, spectroscopic features characteristic of the parallel beta helix topology in the pectate lyases are present in the circular dichroic spectrum of internalin A. Altogether, the data support the hypothesis that sequence search patterns can be used to identify proteins, including a subset of LRR proteins, that are likely to fold into the parallel beta helix.
Xenon gas can be used as a heavy atom for determining phases in a protein. We demonstrate that an interpretable electron density map can be obtained for sperm whale metmyoglobin from a single xenon derivative using iterative single isomorphous replacement with the anomalous scattering method.
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