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To our knowledge, a separate, non-catalytic metal-binding do-
main has never been observed in 2KG oxygenases. Because the
N-terminal zinc-binding domain of GBBH does not appear to have
any assigned function in the literature, we performed a search in
the DALI server to identify proteins with a similar fold. The domain
appears to be related to the DUF971 superfamily, which consists of
several short bacterial proteins with unknown functions. Some of
the DUF971 proteins have conserved cysteines in the same posi-
tions as in the GBBH zinc-binding motif. In the Protein Data Bank,
the only structure assigned to the DUF971 family is the entry
3LUU, which contains coordinates of a protein of unknown func-
tion from Acidithiobacillus ferroxidans. 3LUU has a very similar fold
and 18% sequence identity to the GBBH N-terminal domain, and
the Ca atom r.m.s.d. is 2.3 Å, with 83 residues aligned out of 89.
Interestingly, 3LUU also has a bound zinc ion but in a completely
different position and involving different residues compared to
GBBH. The zinc binding residues in GBBH are partially conserved
in 3LUU; one cysteine is replaced with an isoleucine, which seems
to be enough to prevent the coordination of a zinc ion. Apparently,
the zinc ion has an important role in stabilizing the b-sheet-inter-
connecting loop because it is ordered in GBBH but largely disor-
dered (unmodelled) in 3LUU. The closest relative to 3LUU (46%
sequence identity) with a known function is phosphoribosylformi-
mino-5-aminoimidazole carboxamide ribotide isomerase from
Ralstonia solanacearum. It remains to be investigated whether the
actual function of the GBBH N-terminal domain is related to the
above-mentioned proteins.
The GBBH residues involved in zinc binding are evolutionary
conserved in all sequenced eukaryotes more complex than Caeno-
rhabditis elegans. The zinc-binding motif is also conserved in some
yeast and bacterial enzymes, for example, GBBHs from Candida
albicans and Pseudomonas sp. A related enzyme, trimethyllysine
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4. Conclusions
The crystal structure of GBBH apo form has been solved at 2.0 Å
resolution. The GBBH macromolecule contains two identical
monomers with an extensive dimerization surface. The structure
of the catalytic domain of GBBH is similar to other related enzymes
and possesses conserved features, such as Fe(II) and 2KG binding
residues. The fold of the N-terminal domain is novel to 2KG oxy-
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Acknowledgments
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A macromolecule modeling
This work was supported by the Latvian State Research Program
4VPP-2010-6/3.3 and by ESF grant 1DP/1.1.1.2.0/09/APIA/VIAA/
150. We thank Anna Janson and Ana-Laura Stern for their assis-
tance in data collection. We thank the personnel for their help dur-
ing our stay at ESRF, in particular Hassan Belrhali for his assistance
in quickly obtaining the first SAD map. We thank also Prof. Lars Lil-
jas for critical reading of this manuscript.
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