3U02 | pdb_00003u02

Crystal Structure of the tRNA modifier TiaS from Pyrococcus furiosus, Northeast Structural Genomics Consortium Target PfR225

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	DUF1743	e3u02D4	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: DUF1743	ECOD (1.6)
D	TiaS	e3u02D3	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: TiaS	ECOD (1.6)
C	DUF1743	e3u02C2	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: DUF1743	ECOD (1.6)
C	TiaS	e3u02C1	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: TiaS	ECOD (1.6)
B	DUF1743	e3u02B4	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: DUF1743	ECOD (1.6)
B	TiaS	e3u02B3	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: TiaS	ECOD (1.6)
A	DUF1743	e3u02A2	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: DUF1743	ECOD (1.6)
A	TiaS	e3u02A1	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: TiaS	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.70.2200	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.2.0)
D	3.90.600.20	Alpha Beta	Alpha-Beta Complex	Glycinamide Ribonucleotide Synthetase	Chain A, domain 4	CATH (4.2.0)
C	3.30.70.2200	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.2.0)
C	3.90.600.20	Alpha Beta	Alpha-Beta Complex	Glycinamide Ribonucleotide Synthetase	Chain A, domain 4	CATH (4.2.0)
B	3.30.70.2200	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.2.0)
B	3.90.600.20	Alpha Beta	Alpha-Beta Complex	Glycinamide Ribonucleotide Synthetase	Chain A, domain 4	CATH (4.2.0)
A	3.30.70.2200	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.2.0)
A	3.90.600.20	Alpha Beta	Alpha-Beta Complex	Glycinamide Ribonucleotide Synthetase	Chain A, domain 4	CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF22641	TiaS TCKD domain (TiaS_TCKD)	TiaS TCKD domain	This domain is found in tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS and related proteins. TiaS is an ATP-dependent agmatine transferase that catalyses the formation of 2-agmatinylcytidine (agm2C) at the wobble position (C34) of tRNA(Ile2) [1]. Thi ...	This domain is found in tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS and related proteins. TiaS is an ATP-dependent agmatine transferase that catalyses the formation of 2-agmatinylcytidine (agm2C) at the wobble position (C34) of tRNA(Ile2) [1]. This domain is found at the N-terminal of TiaS and it is responsible for ATP binding [1,2].	Domain
A, B, C, D	PF08489	TiaS FLD domain (TiaS_FLD)	TiaS FLD domain	This is the FLD domain found in tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS. TiaS is an archaeal ATP-dependent agmatine transferase that catalyses the formation of 2-agmatinylcytidine (agm2C) at the wobble position (C34) of tRNA(Ile2) [1-3]. This ...	This is the FLD domain found in tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS. TiaS is an archaeal ATP-dependent agmatine transferase that catalyses the formation of 2-agmatinylcytidine (agm2C) at the wobble position (C34) of tRNA(Ile2) [1-3]. This modified base specifically recognises AUA codons. TiaS consists of four domains, the TCKD domain (Pfam:PF22641) at the N-terminal followed by the FLD domain, an OB fold domain and a zinc ribbon domain (ZRD) domain at the C-terminal [2]. This domain is responsible for agmantine binding [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Putative transcription-associated protein TFIIS	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding nucleic acid binding catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity	tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing macromolecule modification tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process 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 cytosine 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, C, D	IPR055394	TiaS, C-terminal zinc ribbon domain	Domain
A, B, C, D	IPR013696	TiaS, FLD domain	Domain
A, B, C, D	IPR004365	OB-fold nucleic acid binding domain, AA-tRNA synthetase-type	Domain
A, B, C, D	IPR053434	tRNA(Ile2) 2-agmatinylcytidine synthetase	Family
A, B, C, D	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A, B, C, D	IPR024913	tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS	Family
A, B, C, D	IPR053870	TiaS-like, TCKD domain	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D	MSE	Parent Component: MET
A, B, C, D	TPO	Parent Component: THR RESID: AA0038 PSI-MOD : O-phospho-L-threonine MOD:00047

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.