2ZPA | pdb_00002zpa

Crystal Structure of tRNA(Met) Cytidine Acetyltransferase

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	UNK_F_TYPE	e2zpaA3	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: UNK_F_TYPE	ECOD (1.6)
A	GNAT_acetyltr_2	e2zpaA1	A: a+b three layers	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat) (From Topology)	T: Acyl-CoA N-acyltransferases (Nat)	F: GNAT_acetyltr_2	ECOD (1.6)
A	DUF1726	e2zpaA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DUF1726	ECOD (1.6)
A	Helicase_RecD	e2zpaA4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_RecD	ECOD (1.6)
B	UNK_F_TYPE	e2zpaB4	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: UNK_F_TYPE	ECOD (1.6)
B	GNAT_acetyltr_2	e2zpaB3	A: a+b three layers	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat) (From Topology)	T: Acyl-CoA N-acyltransferases (Nat)	F: GNAT_acetyltr_2	ECOD (1.6)
B	DUF1726	e2zpaB6	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DUF1726	ECOD (1.6)
B	Helicase_RecD	e2zpaB5	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_RecD	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.11040	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	3.40.630.30	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Gcn5-related N-acetyltransferase (GNAT)	CATH (4.3.0)
A	1.20.120.890	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	tRNA(Met) cytidine acetyltransferase, tail domain	CATH (4.3.0)
B	3.40.50.11040	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	3.40.630.30	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Gcn5-related N-acetyltransferase (GNAT)	CATH (4.3.0)
B	1.20.120.890	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	tRNA(Met) cytidine acetyltransferase, tail domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF17176	tRNA-binding domain (tRNA_bind_3)	tRNA-binding domain	This domain, found at the C-terminus of tRNA(Met) cytidine acyltransferase, may be involved in tRNA-binding [1]. This family represents the tRNA-binding domain proteins not captured by Pfam:PF13725.	Domain
A, B	PF08351	tRNA(Met) cytidine acetyltransferase TmcA, N-terminal (TmcA_N)	tRNA(Met) cytidine acetyltransferase TmcA, N-terminal	This domain of unknown function is often found at the N-terminus of the bacterial tRNA(Met) cytidine acetyltransferase TmcA. TmcA catalyses the formation of N(4)-acetylcytidine (ac4C) at the wobble position of tRNA(Met) by using acetyl-CoA as an acet ...	This domain of unknown function is often found at the N-terminus of the bacterial tRNA(Met) cytidine acetyltransferase TmcA. TmcA catalyses the formation of N(4)-acetylcytidine (ac4C) at the wobble position of tRNA(Met) by using acetyl-CoA as an acetyl donor and either ATP or GTP [1,2,5]. This modification is thought to ensure precise recognition of the AUG codon by strengthening C-G base-pair interaction and also prevent misrecognition of the near cognate AUA codon [1]. This domain is also found in mammalian N-acetyltransferase 10 (NAT10) and fungal protein Kre33. Kre33 and NAT10 are RNA cytosine acetyltransferases with specificity toward both 18S rRNA and tRNAs and contain additional putative nuclear and nucleolar localization signals (NLS and NoLS respectively) [3,4,5].	Domain
A, B	PF13718	GNAT acetyltransferase 2 (GNAT_acetyltr_2)	GNAT acetyltransferase 2	-	Family
A, B	PF05127	RNA cytidine acetyltransferase NAT10/TcmA, helicase domain (NAT10_TcmA_helicase)	RNA cytidine acetyltransferase NAT10/TcmA, helicase domain	This domain contains a P-loop (Walker A) motif, suggesting that it has ATPase activity, and a Walker B motif. It si found in RNA cytidine acetyltransferase NAT10 from eukaryotes and tRNA(Met) cytidine acetyltransferase TcmA from prokaryotes. NAT10 ca ...	This domain contains a P-loop (Walker A) motif, suggesting that it has ATPase activity, and a Walker B motif. It si found in RNA cytidine acetyltransferase NAT10 from eukaryotes and tRNA(Met) cytidine acetyltransferase TcmA from prokaryotes. NAT10 catalyses the formation of N4-acetylcytidine (ac4C) modification on mRNAs, 18S rRNA and tRNAs [1-4]. In tRNA(Met) cytidine acetyltransferase (TmcA) it may function as an RNA helicase motor (driven by ATP hydrolysis) which delivers the wobble base to the active centre of the GCN5-related N-acetyltransferase (GNAT) domain [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Uncharacterized protein ypfI	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 tRNA cytidine N4-acetyltransferase activity N-acetyltransferase activity acyltransferase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity acetyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups catalytic activity N-acyltransferase activity 18S rRNA cytidine N-acetyltransferase activity peptide 2-hydroxyisobutyryltransferase activity RNA binding tRNA binding nucleic acid binding	ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process maturation of SSU-rRNA cellular component organization or biogenesis RNA processing rRNA metabolic process rRNA acetylation ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process maturation of SSU-rRNA cellular component organization or biogenesis RNA processing rRNA metabolic process rRNA acetylation RNA acetylation rRNA acetylation involved in maturation of SSU-rRNA primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process ribosomal small subunit biogenesis RNA modification biosynthetic process macromolecule modification metabolic process cellular process macromolecule metabolic process tRNA modification tRNA metabolic process tRNA processing tRNA acetylation tRNA wobble cytosine modification tRNA wobble base modification	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR007807	TcmA/NAT10, helicase domain	Domain
A, B	IPR013562	TmcA/NAT10, N-terminal	Domain
A, B	IPR032672	TmcA/NAT10/Kre33	Family
A, B	IPR024914	tRNA(Met) cytidine acetyltransferase TmcA	Family
A, B	IPR000182	GNAT domain	Domain
A, B	IPR033442	tRNA(Met) cytidine acetyltransferase TmcA, tRNA-binding domain	Domain
A, B	IPR038321	TmcA, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR016181	Acyl-CoA N-acyltransferase	Homologous Superfamily
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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.