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Open Access Highly Accessed Research article

LUD, a new protein domain associated with lactate utilization

William C Hwang12*, Constantina Bakolitsa2, Marco Punta3, Penelope C Coggill3, Alex Bateman34, Herbert L Axelrod15, Neil D Rawlings3, Mayya Sedova12, Scott N Peterson2, Ruth Y Eberhardt34, L Aravind6, Jaime Pascual7 and Adam Godzik1289*

Author Affiliations

1 Joint Center for Structural Genomics, La Jolla, CA 92037, USA

2 Sanford Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA

3 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK

4 European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK

5 Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA

6 National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA

7 Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA

8 Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA 92093‑0446, USA

9 Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah 21589, Kingdom of Saudi Arabia

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BMC Bioinformatics 2013, 14:341  doi:10.1186/1471-2105-14-341

Published: 26 November 2013

Abstract

Background

A novel highly conserved protein domain, DUF162 [Pfam: PF02589], can be mapped to two proteins: LutB and LutC. Both proteins are encoded by a highly conserved LutABC operon, which has been implicated in lactate utilization in bacteria. Based on our analysis of its sequence, structure, and recent experimental evidence reported by other groups, we hereby redefine DUF162 as the LUD domain family.

Results

JCSG solved the first crystal structure [PDB:2G40] from the LUD domain family: LutC protein, encoded by ORF DR_1909, of Deinococcus radiodurans. LutC shares features with domains in the functionally diverse ISOCOT superfamily. We have observed that the LUD domain has an increased abundance in the human gut microbiome.

Conclusions

We propose a model for the substrate and cofactor binding and regulation in LUD domain. The significance of LUD-containing proteins in the human gut microbiome, and the implication of lactate metabolism in the radiation-resistance of Deinococcus radiodurans are discussed.

Keywords:
LUD; DUF162; LutB; LutC; Domain of unknown function; Deinococcus radiodurans