{PDOC00363}
{PS50862; AA_TRNA_LIGASE_II}
{PS50860; AA_TRNA_LIGASE_II_ALA}
{PS50861; AA_TRNA_LIGASE_II_GLYAB}
{BEGIN}
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* Aminoacyl-transfer RNA synthetases class-II profiles *
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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 to 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 beta-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.

-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.

-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.

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

-Expert(s) to contact by email:
           Cusack S.; cusack@embl-grenoble.fr

-Last update: May 2002 / Text revised; profiles added; pattern deleted.

[ 1] Schimmel P.
     "Aminoacyl tRNA synthetases: general scheme of structure-function
     relationships in the polypeptides and recognition of transfer RNAs."
     Annu. Rev. Biochem. 56:125-158(1987).
     PubMed=3304131; DOI=10.1146/annurev.bi.56.070187.001013
[ 2] Delarue M., Moras D.
     "The aminoacyl-tRNA synthetase family: modules at work."
     BioEssays 15:675-687(1993).
     PubMed=8274143
[ 3] Schimmel P.
     "Classes of aminoacyl-tRNA synthetases and the establishment of the
     genetic code."
     Trends Biochem. Sci. 16:1-3(1991).
     PubMed=2053131
[ 4] Nagel G.M., Doolittle R.F.
     "Evolution and relatedness in two aminoacyl-tRNA synthetase
     families."
     Proc. Natl. Acad. Sci. U.S.A. 88:8121-8125(1991).
     PubMed=1896459
[ 5] Cusack S., Haertlein M., Leberman R.
     "Sequence, structural and evolutionary relationships between class 2
     aminoacyl-tRNA synthetases."
     Nucleic Acids Res. 19:3489-3498(1991).
     PubMed=1852601
[ 6] Cusack S.
     "Sequence, structure and evolutionary relationships between class 2
     aminoacyl-tRNA synthetases: an update."
     Biochimie 75:1077-1081(1993).
     PubMed=8199242
[ 7] Cusack S., Berthet-Colominas C., Haertlein M., Nassar N., Leberman R.
     "A second class of synthetase structure revealed by X-ray analysis of
     Escherichia coli seryl-tRNA synthetase at 2.5 A."
     Nature 347:249-255(1990).
     PubMed=2205803; DOI=10.1038/347249a0
[ 8] Delarue M.
     "Aminoacyl-tRNA synthetases."
     Curr. Opin. Struct. Biol. 5:48-55(1995).
     PubMed=7773747
[ 9] Leveque F., Plateau P., Dessen P., Blanquet S.
     "Homology of lysS and lysU, the two Escherichia coli genes encoding
     distinct lysyl-tRNA synthetase species."
     Nucleic Acids Res. 18:305-312(1990).
     PubMed=2183178
[10] Nakatsu T., Kato H., Oda J.
     Nat. Struct. Biol. 5:15-19(1998).

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