Literature summary for 7.5.2.3 extracted from

Abe, K.; Sunagawa, N.; Terada, T.; Takahashi, Y.; Arakawa, T.; Igarashi, K.; Samejima, M.; Nakai, H.; Taguchi, H.; Nakajima, M.; Fushinobu, S.
Structural and thermodynamic insights into -1,2-glucooligosaccharide capture by a solute-binding protein in Listeria innocua (2018), J. Biol. Chem., 293, 8812-8828 .

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Crystallization (Commentary)

Crystallization (Comment)	Organism
purified SO-BP, comprisng residues 26-422 without the signal peptide, in a ligand-free form and in complexes with substrates Sop3, Sop4, and Sop5, X-ray diffraction structure determination and analysis at 1.6-2.2 A resolution	Listeria innocua

Protein Variants

Protein Variants	Comment	Organism
D193A	site-directed mutagenesis	Listeria innocua
Q197A	site-directed mutagenesis	Listeria innocua

General Stability

General Stability	Organism
energetic contributions of interactions at unit C to the binding to SO-BP, mo,ecular dynamics, overview	Listeria innocua

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
additional information	-	additional information	sophorooligosaccharide binding kinetics and thermodynamics of wild-type Lin1841 and mutants, overview	Listeria innocua

Localization

Localization	Comment	Organism	GeneOntology No.	Textmining
membrane	contains two transmembrane domains	Listeria innocua	16020	-

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	required	Listeria innocua

Organism

Organism	UniProt	Comment	Textmining
Listeria innocua	Q92AS8	-	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
ATP + H2O + beta-glucan[side 1]	chain length specificity of Lin1841, key factor determining the specificity for chain length of ligands is the polar interactions toward unit C. SO-BP binds to Sopns with energetically favorable conformations	Listeria innocua	ADP + phosphate + beta-glucan[side 2]	-	?
ATP + H2O + sophoropentasaccharide[side 1]	substrate Sop5	Listeria innocua	ADP + phosphate + sophoropentasaccharide[side 2]	-	?
ATP + H2O + sophorotetrasaccharide[side 1]	substrate Sop4	Listeria innocua	ADP + phosphate + sophorotetrasaccharide[side 2]	-	?
ATP + H2O + sophorotrisaccharide[side 1]	substrate Sop3	Listeria innocua	ADP + phosphate + sophorotrisaccharide[side 2]	-	?
additional information	Sopn-binding protein (SO-BP) specifically binds to shorter oligosaccharides (Sopns) with a degree of polymerization of 3 or more, with Kd values in the micromolar range. The enzyme also binds to larger linear beta-1,2-glucans (average DP 25)	Listeria innocua	?	-	?

Subunits

Subunits	Comment	Organism
More	enzyme structure analysis and modeling, enzyme SO-BP is classified in structural cluster D-I of solute-binding proteins, SBPs. The complex structures with substrates Sop3-5s bound can be overlaid well	Listeria innocua

Synonyms

Synonyms	Comment	Organism
Lin1841	-	Listeria innocua
SO-BP	-	Listeria innocua
Sopn-binding protein	-	Listeria innocua

Cofactor

Cofactor	Comment	Organism	Structure
ATP	-	Listeria innocua

General Information

General Information	Comment	Organism
evolution	the ABC uptake system associated with SO-BP is conserved in a number of bacterial species in firmicutes, actinobacteria, and proteobacteria. Consensus phylogenetic tree of SO-BP homologues, the phylogenetic tree is constructed using the neighbor-joining method, overview	Listeria innocua
additional information	the complex structures with substrates Sop3-5s bound can be overlaid well, molecular dynamics and three-dimensional structure modeling, architecture of the ligand-binding site, overview. Hydrogen bonds play a pivotal role in stabilizing the SO-BP-Sopn complexes. Thr95, Thr96, Glu147, and Gly301 form hydrogen bonds with the hydroxyl groups of unit A. Glu45 and Tyr145 form hydrogen bonds with the hydroxyl groups of unit B. Asp193 and Gln197 form hydrogen bonds with the hydroxyl groups at unit C. These interactions are shared among the Sopn-bound structures. Contribution of interactions at unit C to complex stability	Listeria innocua
physiological function	ATP-binding cassette (ABC)2-type transporters are widely distributed in living organisms, forming one of the largest protein superfamilies. ABC transporters utilize the free energy obtained from ATP hydrolysis to import or export a wide variety of molecules across cellular membranes. They share a common architecture consisting of two transmembrane domains (TMDs) and intracellular nucleotide-binding domains (NBDs). In bacterial ABC importers, an additional domain, a solute (or substrate)-binding protein (SBP), serves as an initial receptor that specifically binds to ligands with high affinity, delivers them to TMDs, and stimulates the ATPase activity. Genes Lin1841 and Lin1842-1843 from the Gram-positive bacterium Listeria innocua encode an SBP and TMDs, respectively. The transporter is responsible for uptake of beta-1,2-Glucan and its shorter oligosaccharides (sophorooligosaccharides, Sopns). beta-1,2-Glucans are bacterial carbohydrates that exist in cyclic or linear forms and play an important role in infections and symbioses involving Gram-negative bacteria. Sopns are captured and imported into the bacterial cell by Sopn-binding protein (SO-BP, Lin1841) associated with the ATP-binding cassette (ABC) transporter. A key factor determining the specificity for chain length of ligands is the polar interactions toward unit C	Listeria innocua

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Release 2023.1 (January 2023)