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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.

Show MeSH
Domain organization of LUD domain. a. The most common domain organizations of LUD domain are shown. While predominantly found to exist by itself, LUD domain is also frequently found together with domains such as 4Fe-4S dicluster domain Fer4_8 [Pfam:PF13183], DUF3390 [Pfam:PF11870], cysteine-rich iron-sulfur binding cluster domain CCG [Pfam:PF02754]. b. Pie chart showing the frequency of common LUD domain organizations in known proteins.
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Figure 3: Domain organization of LUD domain. a. The most common domain organizations of LUD domain are shown. While predominantly found to exist by itself, LUD domain is also frequently found together with domains such as 4Fe-4S dicluster domain Fer4_8 [Pfam:PF13183], DUF3390 [Pfam:PF11870], cysteine-rich iron-sulfur binding cluster domain CCG [Pfam:PF02754]. b. Pie chart showing the frequency of common LUD domain organizations in known proteins.

Mentions: While predominantly found to exist by itself, LUD domain is also frequently found together with domains such as the 4Fe-4S dicluster domain Fer4_8 [Pfam: PF13183], DUF3390 [Pfam: PF11870], and cysteine-rich iron-sulfur binding cluster domain CCG [Pfam: PF02754] [17]. FigureĀ 3 shows the most common domain architectures featuring the LUD domain according to Pfam release 27.0.


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)

Domain organization of LUD domain. a. The most common domain organizations of LUD domain are shown. While predominantly found to exist by itself, LUD domain is also frequently found together with domains such as 4Fe-4S dicluster domain Fer4_8 [Pfam:PF13183], DUF3390 [Pfam:PF11870], cysteine-rich iron-sulfur binding cluster domain CCG [Pfam:PF02754]. b. Pie chart showing the frequency of common LUD domain organizations in known proteins.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Domain organization of LUD domain. a. The most common domain organizations of LUD domain are shown. While predominantly found to exist by itself, LUD domain is also frequently found together with domains such as 4Fe-4S dicluster domain Fer4_8 [Pfam:PF13183], DUF3390 [Pfam:PF11870], cysteine-rich iron-sulfur binding cluster domain CCG [Pfam:PF02754]. b. Pie chart showing the frequency of common LUD domain organizations in known proteins.
Mentions: While predominantly found to exist by itself, LUD domain is also frequently found together with domains such as the 4Fe-4S dicluster domain Fer4_8 [Pfam: PF13183], DUF3390 [Pfam: PF11870], and cysteine-rich iron-sulfur binding cluster domain CCG [Pfam: PF02754] [17]. FigureĀ 3 shows the most common domain architectures featuring the LUD domain according to Pfam release 27.0.

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