4xfr | pdb_00004xfr

Crystal structure of a domain of unknown function (DUF1537) from Bordetella bronchiseptica (BB3215), Target EFI-511620, with bound citrate, domain swapped dimer, space group P6522

spinqualitylabelsall models 4xfr, resolution 2.00Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4xfr is a 2 chain structure with sequence from Bordetella bronchiseptica RB50. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2Å Ligands: CIT, MSE Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function DTNK_BORBR Catalyzes the ATP-dependent phosphorylation of D-threonate to D-threonate 4-phosphate. Can also phosphorylate 4-hydroxy-L-threonine, with lower efficiency. Publication Abstract from PubMed Using a large-scale "genomic enzymology" approach, we (i) assigned novel ATP-dependent four-carbon acid sugar kinase functions to members of the DUF1537 protein family (domain of unknown function; Pfam families PF07005 and PF17042) and (ii) discovered novel catabolic pathways for d-threonate, l-threonate, and d-erythronate. The experimentally determined ligand specificities of several solute binding proteins (SBPs) for TRAP (tripartite ATP-independent permease) transporters for four-carbon acids, including d-erythronate and l-erythronate, were used to constrain the substrates for the catabolic pathways that degrade the SBP ligands to intermediates in central carbon metabolism. Sequence similarity networks and genome neighborhood networks were used to identify the enzyme components of the pathways. Conserved genome neighborhoods encoded SBPs as well as permease components of the TRAP transporters, members of the DUF1537 family, and a member of the 4-hydroxy-l-threonine 4-phosphate dehydrogenase (PdxA) oxidative decarboxylase, class II aldolase, or ribulose 1,5-bisphosphate carboxylase/oxygenase, large subunit (RuBisCO) superfamily. Because the characterized substrates of members of the PdxA, class II aldolase, and RuBisCO superfamilies are phosphorylated, we postulated that the members of the DUF1537 family are novel ATP-dependent kinases that participate in catabolic pathways for four-carbon acid sugars. We determined that (i) the DUF1537/PdxA pair participates in a pathway for the conversion of d-threonate to dihydroxyacetone phosphate and CO2 and (ii) the DUF1537/class II aldolase pair participates in pathways for the conversion of d-erythronate and l-threonate (epimers at carbon-3) to dihydroxyacetone phosphate and CO2 The physiological importance of these pathways was demonstrated in vivo by phenotypic and genetic analyses. Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars.,Zhang X, Carter MS, Vetting MW, San Francisco B, Zhao S, Al-Obaidi NF, Solbiati JO, Thiaville JJ, de Crecy-Lagard V, Jacobson MP, Almo SC, Gerlt JA Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):E4161-9. doi:, 10.1073/pnas.1605546113. Epub 2016 Jul 11. PMID:27402745 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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