The crystal structure of affinity-purified Thermomonospora fusca beta -mann
anase has been solved despite the lack of the major part of the amino-acid
sequence. A high-quality electron-density map allowed the identification of
a stretch of eight amino acids close to the C-terminus which was used to d
esign a degenerate downstream PCR primer. Together with a specific primer p
reviously derived from the N-terminus, 95.7% of the mannanase gene sequence
was obtained from genomic T. fusca DNA by PCR. The structure-derived seque
nce was then compared with the DNA-derived sequence and corrected when nece
ssary. Applying the presented protocol, there was no need to manually build
a model at an early stage of structure determination, an erroneous and ted
ious process, especially in the absence of the amino-acid sequence. Using t
he DNA sequence information and the current version of ARP/wARP, 281 residu
es, or 93% of the polypeptide chain (including side chains), were built and
refined to an R factor of 16.5% without any manual intervention.