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Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases [ 47322]
Superfamily:   Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases [ 47323]
Families:   Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases [ 47324] (6)


Superfamily statistics
Genomes (3,257) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 23,726 126,155 14
Proteins 23,281 123,986 14


Functional annotation
General category Information
Detailed category Translation

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0 Least Informative Direct
Biological Process (BP) primary metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0000000000001602 Least Informative Direct
Biological Process (BP) peptide metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) amide biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) tRNA metabolic process 0 Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.2272 Moderately Informative Inherited
Molecular Function (MF) ligase activity 0 Informative Direct
Molecular Function (MF) RNA binding 0.0001813 Informative Direct
Cellular Component (CC) protein complex 0.00005872 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.0001785 Least Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.08199 Least Informative Inherited
Cellular Component (CC) plastid 0.00001238 Informative Direct
Cellular Component (CC) chloroplast stroma 0.00001792 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Least InformativeDirect
Enzyme Commission (EC)Ligases forming aminoacyl-tRNA and related compoun0Moderately InformativeDirect
Enzyme Commission (EC)Forming carbon-nitrogen bonds1Moderately InformativeInherited
Enzyme Commission (EC)Valine--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Isoleucine--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Methionine--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Leucine--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Arginine--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Acid--ammonia (or amide) ligases (amide synthases)0.9871Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processProtein biosynthesis0InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationRNA-binding1Moderately InformativeInherited
Post-translational modificationAminoacyl-tRNA synthetase0InformativeDirect
Post-translational modificationtRNA-binding0Highly InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009080 SSF47323 Protein matches
Abstract

The twenty aminoacyl-tRNA synthetases catalyse the attachment of an amino acid to its cognate transfer RNA (tRNA) molecule in a highly specific two-step reaction. All of these proteins fall into one of two classes comprised of ten enzymes each: class 1 (Arg, Cys, Glu, Gln, Ile, Leu, Met, Tyr, Trp and Val) and class 2 (Ala, Asn, Gly, His, Lys, Phe, Pro, Ser, and Thr). Class 1 enzymes are mostly monomeric, and contain a characteristic Rossman binding fold that bind the tRNA acceptor stem from the minor groove side, using two highly conserved sequences. In contrast, class 2 enzymes share an anti-parallel beta-sheet formation that binds to the major groove side of the acceptor stem. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Class 1a (Arg, Cys, Ile, Leu, Met, Val) possess an RNA-binding domain with an alpha-helix-bundle fold; the binding of the anticodon of tRNA to the RNA-binding domain induces a conformation change in the catalytic domain of the enzyme [PubMed10993737].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 10 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 10 hidden Markov models representing the Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]