Literature summary for 2.6.1.B18 extracted from

Mei, X.; Alvarez, J.; Bon Ramos, A.; Samanta, U.; Iwata-Reuyl, D.; Swairjo, M.A.
Crystal structure of the archaeosine synthase QueF-like-Insights into amidino transfer and tRNA recognition by the tunnel fold (2017), Proteins, 85, 103-116 .

Search for more literature for 2.6.1.B18

Cloned(Commentary)

Cloned (Comment)	Organism
-	Pyrobaculum calidifontis
gene queF-L, recombinant overexpression of His6-tagged enzyme, possessing a factor Xa cleavage site, in Escherichia coli	Pyrobaculum calidifontis

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified recombinant wild-type or SeMet-labeled enzyme in complex with preQ0, hanging drop vapour diffusion method, mixing of 0.001 ml of protein solution with 0.001 ml of reservoir solution containing 17-19% PEG 3350, 0.15 M potassium thiocyanate, and 0.05% sodium azide, and equilibration against 0.5 mL of reservoir solution, for the SeMet-labeled protein in complex with preQ0, the same conditions are used, except crystallization is conducted in sitting drops set up by mixing 0.002 ml of protein solution with 0.001 ml of reservoir solution, 20°C, 1-2 weeks, X-ray diffraction structure determination and analysis at 1.91 A and 2.74 A resolution, respectively, modelling	Pyrobaculum calidifontis
structure in the presence of preQ0, reveals a symmetric T-fold homodecamer of two head-to-head facing pentameric subunits, with 10 active sites at the inter-monomer interfaces. Bound preQ0 forms a stable covalent thioimide bond with a conserved active site cysteine. QueF-L lacks a NADPH binding site	Pyrobaculum calidifontis

Crystallization (Comment)

Organism

purified recombinant wild-type or SeMet-labeled enzyme in complex with preQ0, hanging drop vapour diffusion method, mixing of 0.001 ml of protein solution with 0.001 ml of reservoir solution containing 17-19% PEG 3350, 0.15 M potassium thiocyanate, and 0.05% sodium azide, and equilibration against 0.5 mL of reservoir solution, for the SeMet-labeled protein in complex with preQ0, the same conditions are used, except crystallization is conducted in sitting drops set up by mixing 0.002 ml of protein solution with 0.001 ml of reservoir solution, 20°C, 1-2 weeks, X-ray diffraction structure determination and analysis at 1.91 A and 2.74 A resolution, respectively, modelling

Pyrobaculum calidifontis

structure in the presence of preQ0, reveals a symmetric T-fold homodecamer of two head-to-head facing pentameric subunits, with 10 active sites at the inter-monomer interfaces. Bound preQ0 forms a stable covalent thioimide bond with a conserved active site cysteine. QueF-L lacks a NADPH binding site

Pyrobaculum calidifontis

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.
7-cyano-7-carbaguanine in tRNA + NH3	Pyrobaculum calidifontis	-	7-carboximidamide-guanine in tRNA	-	?
7-cyano-7-carbaguanine in tRNA + NH3	Pyrobaculum calidifontis JCM 11548	-	7-carboximidamide-guanine in tRNA	-	?
7-cyano-7-carbaguanine in tRNA + NH3	Pyrobaculum calidifontis VA1	-	7-carboximidamide-guanine in tRNA	-	?

Organism

Organism	UniProt	Comment	Textmining
Pyrobaculum calidifontis	A3MSP1	-	-
Pyrobaculum calidifontis JCM 11548	A3MSP1	-	-
Pyrobaculum calidifontis VA1	A3MSP1	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant His6-tagged enzyme from Escherichia coli by heat treatment for 15 min at 65°C, nickel affinity chromatography, ultrafiltration, and dialysis, the tag is cleaved off by Factor Xa, followed by another step of nickel affinity chromatography	Pyrobaculum calidifontis

Reaction

Reaction	Comment	Organism	Reaction ID
7-cyano-7-carbaguanine in tRNA + NH3 = 7-carboximidamide-guanine in tRNA	Asp28 deprotonates Cys21, enabling it to nucleophilically attack the nitrile carbon of preQ0 to produce the covalent thioimide intermediate. The ammonium cation, binding in the pocket defined by Asp28 and the pi-system of Tyr90, is deprotonated by Asp28, allowing the neutral ammonia to attack the thioimide carbon from the Tyr90 side (the face of preQ0 facing the protein core). Proton transfers appear to be facilitated in this process via a tightly bound water molecule observed in the preQ0-bound structure that is H-bonded to His62 and the thioimide nitrogen atom. Collapse of the resulting diaminothioorthoester intermediate via cleavage of the carbon-sulfur bond then provides archaeosine-modified tRNA	Pyrobaculum calidifontis	a

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
7-cyano-7-carbaguanine in tRNA + NH3	-	Pyrobaculum calidifontis	7-carboximidamide-guanine in tRNA	-	?
7-cyano-7-carbaguanine in tRNA + NH3	-	Pyrobaculum calidifontis JCM 11548	7-carboximidamide-guanine in tRNA	-	?
7-cyano-7-carbaguanine in tRNA + NH3	-	Pyrobaculum calidifontis VA1	7-carboximidamide-guanine in tRNA	-	?
additional information	substrate binding structures, overview	Pyrobaculum calidifontis	?	-	-
additional information	QueF-L catalyzes the conversion of the nitrile group of the 7-cyano-7-deazaguanine (preQ0 ) base of preQ0-modified tRNA to a formamidino group	Pyrobaculum calidifontis	?	-	?
additional information	substrate binding structures, overview	Pyrobaculum calidifontis JCM 11548	?	-	-
additional information	QueF-L catalyzes the conversion of the nitrile group of the 7-cyano-7-deazaguanine (preQ0 ) base of preQ0-modified tRNA to a formamidino group	Pyrobaculum calidifontis JCM 11548	?	-	?
additional information	substrate binding structures, overview	Pyrobaculum calidifontis VA1	?	-	-
additional information	QueF-L catalyzes the conversion of the nitrile group of the 7-cyano-7-deazaguanine (preQ0 ) base of preQ0-modified tRNA to a formamidino group	Pyrobaculum calidifontis VA1	?	-	?

Subunits

Subunits	Comment	Organism
decamer	-	Pyrobaculum calidifontis

Synonyms

Synonyms	Comment	Organism
amidinotransferase QueF-Like	-	Pyrobaculum calidifontis
ammonium:preQ0-tRNA aminotransferase	UniProt	Pyrobaculum calidifontis
Pcal_0221	locus name	Pyrobaculum calidifontis
QueF-L	-	Pyrobaculum calidifontis
QueF-like	-	Pyrobaculum calidifontis

General Information

General Information	Comment	Organism
evolution	despite distinct catalytic functions, phylogenetic distributions, and only 19% sequence identity, the two enzymes, QueF and QueF-L, share a common preQ0 binding pocket, and likely a common mechanism of thioimide formation. Due to tight twisting of its decamer, QueF-L lacks the NADPH binding site present in QueF. But like QueF, QueF-L possesses an active-site cysteine that serves as a catalytic nucleophile, reacting with the nitrile group to form a covalent thioimide intermediate. The enzymes belong to the tunneling-fold (T-fold) structural superfamily. QueF-L and QueF (from Bacillus subtilis, PDB ID 4F8B, and Vibrio cholerae, PDB ID 3UXJ) exhibit 18-20% sequence identity, structure comparison, detailed overview. The preQ0-binding pocket is defined by a cleft between two subunits from the same pentamer. QueF (EC 1.7.1.13) is unique to bacteria and the Q branch of the pathway and catalyzes the NADPH-dependent reduction of the nitrile group of preQ0 to the amine of preQ1	Pyrobaculum calidifontis
metabolism	the amidinotransferase QueF-Like (QueF-L), responsible for the final step in the biosynthesis of archaeosine in the D-loop of tRNA in a subset of Crenarchaeota. The archaeal homologue of QueF, QueF-Like (QueF-L), found in a subset of Crenarchaeota that lack ArcS, is capable of producing G+-modified tRNA	Pyrobaculum calidifontis
additional information	in the presence of preQ0, the enzyme reveals a symmetric T-fold homodecamer of two head-to-head facing pentameric subunits, with 10 active sites at the inter-monomer interfaces. Bound preQ0 forms a stable covalent thioimide bond with a conserved active site cysteine similar to the intermediate previously observed in the nitrile reductase QueF. Due to tight twisting of its decamer, QueF-L lacks the NADPH binding site present in QueF. A large positively charged molecular surface and a docking model suggest simultaneous binding of multiple tRNA molecules and structure-specific recognition of the D-loop by a surface groove. Ligand docking study of wild-type and SeMet-labeled enzyme, overview	Pyrobaculum calidifontis
physiological function	QueF-L catalyzes the conversion of the nitrile group of the 7-cyano-7-deazaguanine (preQ0) base of preQ0-modified tRNA to a formamidino group	Pyrobaculum calidifontis