Abstract
The crystal structure of Dhaf4260 from Desulfitobacterium hafniense DCB-2 was determined by single-wavelength anomalous diffraction (SAD) to a resolution of 2.01 Å using the semi-automated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). This protein structure is the first representative of the PF04016 (DUF364) Pfam family and reveals a novel combination of two well known domains (an enolase N-terminal-like fold followed by a Rossmann-like domain). Structural and bioinformatic analyses reveal partial similarities to Rossmann-like methyltransferases, with residues from the enolase-like fold combining to form a unique active site that is likely to be involved in the condensation or hydrolysis of molecules implicated in the synthesis of flavins, pterins or other siderophores. The genome context of Dhaf4260 and homologs additionally supports a role in heavy-metal chelation.
Highlights
To extend the structural coverage of proteins for which the biological function is unknown and cannot be deduced by homology, targets were selected from the Pfam (Finn et al, 2008) protein family PF04016 (DUF364)
DUF364 homologs are encountered in proteobacteria, firmicutes, actinobacteria, cyanobacteria, thermotogae and a number of archaea
Analysis of the genetic context and interdomain cleft suggest a role in heavy-metal uptake, possibly involving the synthesis of a flavin or pterin derivative
Summary
To extend the structural coverage of proteins for which the biological function is unknown and cannot be deduced by homology (i.e. domains of unknown function; DUFs), targets were selected from the Pfam (Finn et al, 2008) protein family PF04016 (DUF364). DUF364 homologs are encountered in proteobacteria, firmicutes, actinobacteria, cyanobacteria, thermotogae and a number of archaea. We report the crystal structure of Dhaf4260, the first structural representative of this family, which was determined using the semiautomated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG; http://www.jcsg.org; Lesley et al, 2002) as part of the NIGMS Protein Structure Initiative (PSI). The Dhaf4260 gene of Desulfitobacterium hafniense DCB-2 encodes a protein with a molecular weight of 27.7 kDa (residues 1–251) and a calculated isoelectric point of 5.6. Desulfitobacterium spp. are anaerobic bacteria that are capable of dehalogenating organic compounds and have been studied for their potential in bioremediation processes (Villemur et al, 2006; El Fantroussi et al, 1998)
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