4XGJ

Crystal structure of a domain of unknown function (DUF1537) from Pectobacterium atrosepticum (ECA3761), Target EFI-511609, APO structure, domain swapped dimer

Summary for 4XGJ

• Entry DOI: 10.2210/pdb4xgj/pdb
• Descriptor: Uncharacterized protein (2 entities in total)
• Functional Keywords: enzyme function initiative, efi, structural genomics, unknown function
• Biological source: Pectobacterium atrosepticum
• Total number of polymer chains: 1
• Total formula weight: 49559.85

Authors

Vetting, M.W.,Al Obaidi, N.F.,Toro, R.,Morisco, L.L.,Benach, J.,Wasserman, S.R.,Attonito, J.D.,Scott Glenn, A.,Chamala, S.,Chowdhury, S.,Lafleur, J.,Love, J.,Seidel, R.D.,Whalen, K.L.,Gerlt, J.A.,Almo, S.C.,Enzyme Function Initiative (EFI) (deposition date: 2014-12-30, release date: 2015-02-18, Last modification date: 2024-10-23)

Primary citation

Zhang, X.,Carter, M.S.,Vetting, M.W.,San Francisco, B.,Zhao, S.,Al-Obaidi, N.F.,Solbiati, J.O.,Thiaville, J.J.,de Crecy-Lagard, V.,Jacobson, M.P.,Almo, S.C.,Gerlt, J.A.
Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars.
Proc.Natl.Acad.Sci.USA, 113:E4161-E4169, 2016

PubMed Abstract: 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.

PubMed: 27402745
DOI: 10.1073/pnas.1605546113

Experimental method

X-RAY DIFFRACTION (1.9 Å)