Literature summary for 3.6.5.2 extracted from

Knihtila, R.; Volmar, A.Y.; Meilleur, F.; Mattos, C.
Titration of ionizable groups in proteins using multiple neutron data sets from a single crystal application to the small GTPase Ras (2019), Acta Crystallogr. Sect. F, 75, 111-115 .

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified enzyme hydrogenated H-RAS, residues 1-166, Sitting drop vapour diffusion, 1:1 ratio of protein solution, containing 20 mM HEPES, pH 7.5, 50 mM NaCl, 5 mM MgCl2, 1 mM DTT, and reservoir solution containing 200 mM calcium acetate, 20% w/v PEG 3350, 0.1% w/v n-octyl-beta-D-glucoside. Once the crystals has stopped growing, the hydrogenated reservoir solution is replaced with an identical reservoir solution prepared with D2O. A single crystal of the small GTPase Ras is used to collect three neutron data sets at pD 8.4, 9.0 and 9.4, in crystallo titration study using neutron protein crystallography (NPC), a method that lacks radiation damage of the cyrstals. Structure analysis at resolution of 1.9-2.1 A	Homo sapiens

Crystallization (Comment)

Organism

purified enzyme hydrogenated H-RAS, residues 1-166, Sitting drop vapour diffusion, 1:1 ratio of protein solution, containing 20 mM HEPES, pH 7.5, 50 mM NaCl, 5 mM MgCl2, 1 mM DTT, and reservoir solution containing 200 mM calcium acetate, 20% w/v PEG 3350, 0.1% w/v n-octyl-beta-D-glucoside. Once the crystals has stopped growing, the hydrogenated reservoir solution is replaced with an identical reservoir solution prepared with D2O. A single crystal of the small GTPase Ras is used to collect three neutron data sets at pD 8.4, 9.0 and 9.4, in crystallo titration study using neutron protein crystallography (NPC), a method that lacks radiation damage of the cyrstals. Structure analysis at resolution of 1.9-2.1 A

Homo sapiens

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Ca2+	required	Homo sapiens
Mg2+	required	Homo sapiens

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
GTP + H2O	Homo sapiens	-	GDP + phosphate	-	?

Organism

Organism	UniProt	Comment	Textmining
Homo sapiens	-	-	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
GTP + H2O	-	Homo sapiens	GDP + phosphate	-	?
additional information	Ras binds guanine nucleotides in its guanine nucleotide-binding cleft composed of G-box elements that are conserved among all GTPase proteins	Homo sapiens	?	-	-

Synonyms

Synonyms	Comment	Organism
RAS	-	Homo sapiens
small GTPase	-	Homo sapiens

General Information

General Information	Comment	Organism
additional information	enzyme structure-activity analysis and Ras allosteric networks, detailed overview. The allosteric networks on Ras intimately link switch I and switch II to each other and to two other functionally important regions on the opposite side of the protein. Switch I is linked to helix 5 membrane-interacting residues at the back of the molecule, where Arg161 and Arg164 make salt bridges with the interswitch loop 3 residues Asp47 and Glu49. Switch II is normally disordered and disconnected from the network. When calcium and a negatively charged ligand bind, helix 3 shifts towards helix 4, and the entire switch II becomes ordered and linked to the Ca2+-binding pocket through an extensive water-mediated network	Homo sapiens