1IT8

Crystal structure of archaeosine tRNA-guanine transglycosylase from Pyrococcus horikoshii complexed with archaeosine precursor, preQ0

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1it8a3	All beta proteins	PUA domain-like	PUA domain-like	PUA domain	Archaeosine tRNA-guanine transglycosylase, C3 domain	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
A	d1it8a1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	tRNA-guanine transglycosylase	tRNA-guanine transglycosylase	Archaeosine tRNA-guanine transglycosylase, N-terminal domain	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
A	d1it8a4	Alpha and beta proteins (a+b)	Cystatin-like	Pre-PUA domain	Archaeosine tRNA-guanine transglycosylase, C2 domain	Archaeosine tRNA-guanine transglycosylase, C2 domain	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
B	d1it8b3	All beta proteins	PUA domain-like	PUA domain-like	PUA domain	Archaeosine tRNA-guanine transglycosylase, C3 domain	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
B	d1it8b1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	tRNA-guanine transglycosylase	tRNA-guanine transglycosylase	Archaeosine tRNA-guanine transglycosylase, N-terminal domain	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
B	d1it8b4	Alpha and beta proteins (a+b)	Cystatin-like	Pre-PUA domain	Archaeosine tRNA-guanine transglycosylase, C2 domain	Archaeosine tRNA-guanine transglycosylase, C2 domain	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Pre-PUA domain	8044405	3001126	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PUA domain-like	8044404	3001015	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	tRNA-guanine transglycosylase	8039623	3000635	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	tRNA-guanine transglycosylase	8039623	3000635	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PUA domain-like	8044404	3001015	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Pre-PUA domain	8044405	3001126	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PUA	e1it8A1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: PUA	ECOD (1.6)
A	TGT_C1	e1it8A2	A: a+b two layers	X: Cystatin-like	H: Pre-PUA domain (From Topology)	T: Pre-PUA domain	F: TGT_C1	ECOD (1.6)
A	TGT	e1it8A3	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: TGT	ECOD (1.6)
B	PUA	e1it8B1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: PUA	ECOD (1.6)
B	TGT_C1	e1it8B2	A: a+b two layers	X: Cystatin-like	H: Pre-PUA domain (From Topology)	T: Pre-PUA domain	F: TGT_C1	ECOD (1.6)
B	TGT	e1it8B3	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: TGT	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.105	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Queuine tRNA-ribosyltransferase-like	CATH (4.3.0)
A	3.90.1020.10	Alpha Beta	Alpha-Beta Complex	Archaeosine Trna-guanine Transglycosylase	Chain: A, domain 2	CATH (4.3.0)
A	3.10.450.90	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
A	2.30.130.10	Mainly Beta	Roll	Archaeosine Trna-guanine Transglycosylase	Chain: A, domain 4	CATH (4.3.0)
B	3.20.20.105	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Queuine tRNA-ribosyltransferase-like	CATH (4.3.0)
B	3.90.1020.10	Alpha Beta	Alpha-Beta Complex	Archaeosine Trna-guanine Transglycosylase	Chain: A, domain 2	CATH (4.3.0)
B	3.10.450.90	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
B	2.30.130.10	Mainly Beta	Roll	Archaeosine Trna-guanine Transglycosylase	Chain: A, domain 4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01702	Queuine tRNA-ribosyltransferase (TGT)	Queuine tRNA-ribosyltransferase	This is a family of queuine tRNA-ribosyltransferases EC:2.4.2.29, also known as tRNA-guanine transglycosylase and guanine insertion enzyme. Queuine tRNA-ribosyltransferase modifies tRNAs for asparagine, aspartic acid, histidine and tyrosine with que ...	This is a family of queuine tRNA-ribosyltransferases EC:2.4.2.29, also known as tRNA-guanine transglycosylase and guanine insertion enzyme. Queuine tRNA-ribosyltransferase modifies tRNAs for asparagine, aspartic acid, histidine and tyrosine with queuine. It catalyses the exchange of guanine-34 at the wobble position with 7-aminomethyl-7-deazaguanine, and the addition of a cyclopentenediol moiety to 7-aminomethyl-7-deazaguanine-34 tRNA; giving a hypermodified base queuine in the wobble position [1,2]. The aligned region contains a zinc binding motif C-x-C-x2-C-x29-H, and important tRNA and 7-aminomethyl-7deazaguanine binding residues [1].	Domain
A, B	PF14809	C1 domain of tRNA-guanine transglycosylase dimerisation (TGT_C1)	C1 domain of tRNA-guanine transglycosylase dimerisation	This short region of the tRNA-guanine transglycosylase enzyme acts as the dimerisation domain of the whole protein [1].	Domain
A, B	PF01472	PUA domain (PUA)	PUA domain	-	Family
A, B	PF14810	Patch-forming domain C2 of tRNA-guanine transglycosylase (TGT_C2)	Patch-forming domain C2 of tRNA-guanine transglycosylase	Domain C2 of tRNA-guanine transglycosylase is formed by a four-stranded anti-parallel beta-sheet lined with two alpha helices. It has conserved basic residues on the surface of the beta-sheets as does the C-terminal domain PUA, Pfam:PF01472. The cata ...	Domain C2 of tRNA-guanine transglycosylase is formed by a four-stranded anti-parallel beta-sheet lined with two alpha helices. It has conserved basic residues on the surface of the beta-sheets as does the C-terminal domain PUA, Pfam:PF01472. The catalytic domain, TGT has conserved basic residues on the outer surface of the N-terminal three-stranded beta sheet, which closes the barrel, and it is postulated that these basic residues from the three domains form a continuous, positively charged patch to which the tRNA binds [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	archaeosine tRNA-guanine transglycosylase	cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding RNA binding nucleic acid binding pentosyltransferase activity glycosyltransferase activity transferase activity catalytic activity	tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA wobble guanine modification tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA wobble guanine modification tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing macromolecule modification tRNA wobble base modification metabolic process cellular process macromolecule metabolic process RNA processing	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR015947	PUA-like superfamily	Homologous Superfamily
A, B	IPR050076	Archaeosine Synthase Type 1/Queuine TRNA-Ribosyltransferase	Family
A, B	IPR004521	Uncharacterised domain CHP00451	Domain
A, B	IPR038370	ArcTGT, C1 domain superfamily	Homologous Superfamily
A, B	IPR036974	PUA domain superfamily	Homologous Superfamily
A, B	IPR029402	tRNA-guanine transglycosylase, patch-forming domain C2	Domain
A, B	IPR004804	tRNA-guanine(15) transglycosylase	Family
A, B	IPR038250	TGT, patch-forming C2 domain superfamily	Homologous Superfamily
A, B	IPR036511	Queuine tRNA-ribosyltransferase-like	Homologous Superfamily
A, B	IPR002616	tRNA-guanine(15) transglycosylase-like	Domain
A, B	IPR002478	PUA domain	Domain
A, B	IPR032729	tRNA-guanine(15) transglycosylase, C1 domain	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.