Literature summary for 3.6.5.3 extracted from

Murakami, R.; Miyoshi, T.; Uchiumi, T.; Ito, K.
Crystal structure of translation initiation factor 5B from the crenarchaeon Aeropyrum pernix (2016), Proteins, 84, 712-717 .

Cloned(Commentary)

Cloned (Comment)	Organism
recombinant expression of C-terminally His6-tagged enzyme in Escherichia coli strain Rosetta(DE3)	Aeropyrum pernix

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified recombinant C-terminally His6-tagged enzyme bound to GDP, 10 mg/ml protein and 1.42 mM GDP in buffer C are heated at 70°C for 10 min prior crystallization, sitting drop vapor diffusion method, mixing of 10 mg/ml protein in 10 mM HEPES-KOH, pH 7.6, 100 mM KCl, 10 mM MgCl2, 1.42 GDP, and 7 mM 2-mercaptoethanol with reservoir solution containing 0.1 M Tris-HCl, pH 7.5, 20% w/v PEG 3000, and 0.2 M calcium acetate, at 20°C, 1 week, X-ray diffraction structure determination and analysis at 1.90 A resolution, molecular replacement using the structure of Methanothermobacter thermautotrophicus aIF5B complexed with GDP (PDB ID 1G7S) as the search model	Aeropyrum pernix

Crystallization (Comment)

Organism

purified recombinant C-terminally His6-tagged enzyme bound to GDP, 10 mg/ml protein and 1.42 mM GDP in buffer C are heated at 70°C for 10 min prior crystallization, sitting drop vapor diffusion method, mixing of 10 mg/ml protein in 10 mM HEPES-KOH, pH 7.6, 100 mM KCl, 10 mM MgCl2, 1.42 GDP, and 7 mM 2-mercaptoethanol with reservoir solution containing 0.1 M Tris-HCl, pH 7.5, 20% w/v PEG 3000, and 0.2 M calcium acetate, at 20°C, 1 week, X-ray diffraction structure determination and analysis at 1.90 A resolution, molecular replacement using the structure of Methanothermobacter thermautotrophicus aIF5B complexed with GDP (PDB ID 1G7S) as the search model

Aeropyrum pernix

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	required	Aeropyrum pernix

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.
GTP + H2O	Aeropyrum pernix	-	GDP + phosphate	-	?
GTP + H2O	Aeropyrum pernix ATCC 700893	-	GDP + phosphate	-	?
GTP + H2O	Aeropyrum pernix DSM 11879	-	GDP + phosphate	-	?
GTP + H2O	Aeropyrum pernix JCM 9820	-	GDP + phosphate	-	?
GTP + H2O	Aeropyrum pernix NBRC 100138	-	GDP + phosphate	-	?

Organism

Organism	UniProt	Comment	Textmining
Aeropyrum pernix	-	-	-
Aeropyrum pernix ATCC 700893	-	-	-
Aeropyrum pernix DSM 11879	-	-	-
Aeropyrum pernix JCM 9820	-	-	-
Aeropyrum pernix NBRC 100138	-	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant C-terminally His6-tagged enzyme from Escherichia coli strain Rosetta(DE3) by heat treatment at 80°C for 20 min, nickel affinity chromatography, dialysis, cation exchange chromatography, followed gel filtration, dialysis, and ultrafiltration	Aeropyrum pernix

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
GTP + H2O	-	Aeropyrum pernix	GDP + phosphate	-	?
GTP + H2O	-	Aeropyrum pernix ATCC 700893	GDP + phosphate	-	?
GTP + H2O	-	Aeropyrum pernix DSM 11879	GDP + phosphate	-	?
GTP + H2O	-	Aeropyrum pernix JCM 9820	GDP + phosphate	-	?
GTP + H2O	-	Aeropyrum pernix NBRC 100138	GDP + phosphate	-	?

Synonyms

Synonyms	Comment	Organism
aIF5B	-	Aeropyrum pernix
IF5B	-	Aeropyrum pernix
infB	-	Aeropyrum pernix
initiation factor 5B	-	Aeropyrum pernix
translation initiation factor 5B	-	Aeropyrum pernix
translational GTPase	-	Aeropyrum pernix

General Information

General Information	Comment	Organism
evolution	different relationships between IF5B and IF1A exist in archaea and eukaryotes, overview	Aeropyrum pernix
additional information	archeal enzyme structure analysis with bound GDP, archaea-specific region of IF5B (helix alpha15) binds and occludes the groove of domain IV, comparison with eukaryotic IF5B enzymes, in which IF5B directly interacts via a groove in its domain IV with initiation factor 1A (IF1A). Archaeal IF5B cannot access IF1A in the same manner as eukaryotic IF5B. Structural comparison of crenarchaeal and euryarchaeal aIF5Bs with crenarchaeal and euryarchaeal, detailed overview	Aeropyrum pernix
physiological function	initiation factor 5B (IF5B) is a universally conserved translational GTPase that catalyzes ribosomal subunit joining	Aeropyrum pernix