Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1 (PBP1), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The origin of PBP module can be traced across the distant phyla, including eukaryotes, archebacteria, and prokaryotes. The majority of PBP2 proteins are involved in the uptake of a variety of soluble substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. The substrate binding domain of the LysR transcriptional regulators and the oligopeptide-like transport systems also contain the type 2 periplasmic binding fold and thus they are significantly homologous to that of the PBP2; however, these two families are grouped into a separate hierarchy of the PBP2 superfamily due to the large number of protein sequences.

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                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1330328838  97 YLNTLgnlPLVeWTIDDKETDIEVSIIQGTPSQLvifNKLFEPLSLTLSPISSAA 151
Cdd:cd13634     9 YLNTL---PLF-YGLEKGKVPPGFELVLGVPSEL---NRMLLEGELDVGLVSSIE 56

The conserved hypothetical protein SCO4506 exhibits the type 2 periplasmic-binidng protein fold; This group includes the SCO4506 protein from Streptomyces coelicolor and related hypothetical proteins. SCO4506 is an ortholog of Ttha1568 (MqnD) from Thermus thermophilies HB8. MqnD is an enzyme within an alternative menaquinone biosynthetic pathway that catalyzes the conversion of cyclic de-hypoxanthine futalosine to 1,4-dihydroxy-6-naphthoate. Menaquinone (MK; vitamin K) is an essential lipid-soluble carrier that shuttles electrons between membrane-bound protein complexes in the electron transport chain. SCO4506 has significant structural homology with the members of type 2 periplasmic-binding fold protein superfamily. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.

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                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1330328838  97 YLNTLgnlPLVeWTIDDKETDIEVSIIQGTPSQLvifNKLFEPLSLTLSPISSAA 151
Cdd:cd13634     9 YLNTL---PLF-YGLEKGKVPPGFELVLGVPSEL---NRMLLEGELDVGLVSSIE 56

Cytochrome c553 [Energy production and conversion];

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1330328838  43 CSTCHGlfAHGGGNVGG---NIRG-------KTLQDINSSLEHESTMKLLSDVLTVKDRQALAMYLNTLGN 103
Cdd:COG2863    25 CAACHG--ADGEGNPGGgapRLAGqhaeylvAQLKAFRSGARKNGVMPAIAKGLSDEDIKALAAYIASLKA 93