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Aminoacyl-tRNA synthetases (EC 6.1.1.-) [1] are a group of enzymes which activate amino acids and transfer them to specific tRNA molecules as the first step in protein biosynthesis. In prokaryotic organisms there are at least twenty different types of aminoacyl-tRNA synthetases, one for each different amino acid. In eukaryotes there are generally two aminoacyl-tRNA synthetases for each different amino acid: one cytosolic form and a mitochondrial form. While all these enzymes have a common function, they are widely diverse in terms of subunit size and of quaternary structure.

The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine are referred to as class-II synthetases [2,3,4,5,6]. Class-II enzymes are generally dimeric or tetrameric, and attach their amino acid to the 3' OH of their tRNA, except for phenylalaninyl-tRNA synthetase which uses the 2' OH like the class-I tRNA synthetase.

Class-II tRNA synthetases are structurally distinct from the class-I enzymes and have a central antiparallel β-sheet instead of the Rossman fold found in Class-I structure (see <PDB:1SES>) [8].

Class-II tRNA synthetases do not share a high degree of similarity, however at least three conserved regions are present [2,5,9]. We have developed three profiles to detect class-II tRNA synthetases. The first one recognize all class-II enzymes except for heterodimeric glycyl-tRNA synthetases and alanyl-tRNA synthetases which are picked up by specific profiles.

There are at least two families of proteins related to class-II enzymes and that are also recognized by the first profile.

• Bacterial aspartate--ammonia ligase (EC 6.3.1.1), the enzyme that produces asparagine from aspartate [10].
• Bacterial ATP phosphoribosyltransferase regulatory subunit (gene hisZ). HisZ seems to allow the regulation of ATP phosphoribosyltransferase activity by histidine. It is distantly related to histidyl-tRNA synthetases and not all members of this family are picked up by the profile.

Cusack S.

May 2002 / Text revised; profiles added; pattern deleted.

PROSITE methods (with tools and information) covered by this documentation:

AA_TRNA_LIGASE_II, PS50862; Aminoacyl-transfer RNA synthetases class-II family profile  (MATRIX)

Sequences known to belong to this class detected by the first profile: ALL, except for heterodimeric glycyl-tRNA synthetases and alanyl-tRNA synthetases Other sequence(s) detected in Swiss-Prot: NONE.

• Domain architecture view of Swiss-Prot proteins matching PS50862 • Retrieve an alignment of Swiss-Prot true positive hits:   Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format • Retrieve the sequence logo from the alignment • Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS50862 • Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS50862 • Scan Swiss-Prot/TrEMBL entries against PS50862 • view ligand binding statistics

Matching PDB structures: 11AS 12AS 1ADJ 1ADY ... [ALL]

AA_TRNA_LIGASE_II_ALA, PS50860; Alanyl-transfer RNA synthetases family profile  (MATRIX)

Sequences known to belong to this class detected by the second profile: ALL heterodimeric glycyl-tRNA synthetases Other sequence(s) detected in Swiss-Prot: NONE.

• Domain architecture view of Swiss-Prot proteins matching PS50860 • Retrieve an alignment of Swiss-Prot true positive hits:   Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format • Retrieve the sequence logo from the alignment • Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS50860 • Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS50860 • Scan Swiss-Prot/TrEMBL entries against PS50860 • view ligand binding statistics

Matching PDB structures: 1RIQ 1YFR 1YFS 1YFT ... [ALL]

AA_TRNA_LIGASE_II_GLYAB, PS50861; Heterodimeric glycyl-transfer RNA synthetases family profile  (MATRIX)

Sequences known to belong to this class detected by the third profile: ALL alanyl-tRNA synthetases Other sequence(s) detected in Swiss-Prot: NONE.

• Domain architecture view of Swiss-Prot proteins matching PS50861 • Retrieve an alignment of Swiss-Prot true positive hits:   Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format • Retrieve the sequence logo from the alignment • Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS50861 • Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS50861 • Scan Swiss-Prot/TrEMBL entries against PS50861 • view ligand binding statistics

Matching PDB structures: 1J5W 3RF1 3RGL 3UFG [ALL]

1	Authors	Schimmel P.
	Title	Aminoacyl tRNA synthetases: general scheme of structure-function relationships in the polypeptides and recognition of transfer RNAs.
	Source	Annu. Rev. Biochem. 56:125-158(1987).
	PubMed ID	3304131
	DOI	10.1146/annurev.bi.56.070187.001013

2	Authors	Delarue M., Moras D.
	Title	The aminoacyl-tRNA synthetase family: modules at work.
	Source	BioEssays 15:675-687(1993).
	PubMed ID	8274143

3	Authors	Schimmel P.
	Title	Classes of aminoacyl-tRNA synthetases and the establishment of the genetic code.
	Source	Trends Biochem. Sci. 16:1-3(1991).
	PubMed ID	2053131

4	Authors	Nagel G.M., Doolittle R.F.
	Title	Evolution and relatedness in two aminoacyl-tRNA synthetase families.
	Source	Proc. Natl. Acad. Sci. U.S.A. 88:8121-8125(1991).
	PubMed ID	1896459

5	Authors	Cusack S., Haertlein M., Leberman R.
	Title	Sequence, structural and evolutionary relationships between class 2 aminoacyl-tRNA synthetases.
	Source	Nucleic Acids Res. 19:3489-3498(1991).
	PubMed ID	1852601

6	Authors	Cusack S.
	Title	Sequence, structure and evolutionary relationships between class 2 aminoacyl-tRNA synthetases: an update.
	Source	Biochimie 75:1077-1081(1993).
	PubMed ID	8199242

7	Authors	Cusack S., Berthet-Colominas C., Haertlein M., Nassar N., Leberman R.
	Title	A second class of synthetase structure revealed by X-ray analysis of Escherichia coli seryl-tRNA synthetase at 2.5 A.
	Source	Nature 347:249-255(1990).
	PubMed ID	2205803
	DOI	10.1038/347249a0

8	Authors	Delarue M.
	Title	Aminoacyl-tRNA synthetases.
	Source	Curr. Opin. Struct. Biol. 5:48-55(1995).
	PubMed ID	7773747

9	Authors	Leveque F., Plateau P., Dessen P., Blanquet S.
	Title	Homology of lysS and lysU, the two Escherichia coli genes encoding distinct lysyl-tRNA synthetase species.
	Source	Nucleic Acids Res. 18:305-312(1990).
	PubMed ID	2183178

10	Authors	Nakatsu T., Kato H., Oda J.
	Source	Nat. Struct. Biol. 5:15-19(1998).

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