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LUD, a new protein domain associated with lactate utilization.

Hwang WC, Bakolitsa C, Punta M, Coggill PC, Bateman A, Axelrod HL, Rawlings ND, Sedova M, Peterson SN, Eberhardt RY, Aravind L, Pascual J, Godzik A - BMC Bioinformatics (2013)

Bottom Line: We have observed that the LUD domain has an increased abundance in the human gut microbiome.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Joint Center for Structural Genomics, La Jolla, CA 92037, USA. wchwang@sanfordburnham.org.

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.

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Structure of LutC protein from Deinococcus radiodurans. The protein structure is shown in cartoon style and colored in rainbow format (N-terminus being blue and C-terminus red). The dashed line in the figure represents a break in the protein polypeptide chain as a result of missing electron density in the protein structure.
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Figure 1: Structure of LutC protein from Deinococcus radiodurans. The protein structure is shown in cartoon style and colored in rainbow format (N-terminus being blue and C-terminus red). The dashed line in the figure represents a break in the protein polypeptide chain as a result of missing electron density in the protein structure.

Mentions: The Joint Center for Structural Genomics (JCSG) determined the first crystal structure of the LUD domain family: LutC protein from Deinococcus radiodurans. The LutC protein structure is a mixed alpha-helix and beta-sheet protein (FigureĀ 1). The protein core is made up of two orthogonal beta-sheets, each consisting of four beta-strands. The alpha-helices are packed against the two solvent-facing surfaces of the beta-sheets as well as against the side openings of the protein core.


LUD, a new protein domain associated with lactate utilization.

Hwang WC, Bakolitsa C, Punta M, Coggill PC, Bateman A, Axelrod HL, Rawlings ND, Sedova M, Peterson SN, Eberhardt RY, Aravind L, Pascual J, Godzik A - BMC Bioinformatics (2013)

Structure of LutC protein from Deinococcus radiodurans. The protein structure is shown in cartoon style and colored in rainbow format (N-terminus being blue and C-terminus red). The dashed line in the figure represents a break in the protein polypeptide chain as a result of missing electron density in the protein structure.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3924224&req=5

Figure 1: Structure of LutC protein from Deinococcus radiodurans. The protein structure is shown in cartoon style and colored in rainbow format (N-terminus being blue and C-terminus red). The dashed line in the figure represents a break in the protein polypeptide chain as a result of missing electron density in the protein structure.
Mentions: The Joint Center for Structural Genomics (JCSG) determined the first crystal structure of the LUD domain family: LutC protein from Deinococcus radiodurans. The LutC protein structure is a mixed alpha-helix and beta-sheet protein (FigureĀ 1). The protein core is made up of two orthogonal beta-sheets, each consisting of four beta-strands. The alpha-helices are packed against the two solvent-facing surfaces of the beta-sheets as well as against the side openings of the protein core.

Bottom Line: We have observed that the LUD domain has an increased abundance in the human gut microbiome.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Joint Center for Structural Genomics, La Jolla, CA 92037, USA. wchwang@sanfordburnham.org.

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.

Show MeSH