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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 (3,250) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 23,592 108,268 14
Proteins 23,148 107,083 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) biosynthetic process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) primary metabolic process 0 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.00000005816 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) amide biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) peptide metabolic process 0 Moderately Informative Direct
Biological Process (BP) organelle organization 0.6135 Moderately Informative Inherited
Biological Process (BP) tRNA metabolic process 0 Informative Direct
Biological Process (BP) mitochondrion organization 0.00003872 Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.08305 Moderately Informative Inherited
Molecular Function (MF) ligase activity 0 Informative Direct
Molecular Function (MF) RNA binding 0.00002372 Informative Direct
Cellular Component (CC) cytoplasmic part 0.0005095 Least Informative Direct
Cellular Component (CC) protein complex 0.5984 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.1848 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0.4352 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 1 Moderately Informative Inherited
Cellular Component (CC) plastid 0.0002098 Informative Direct
Cellular Component (CC) chloroplast stroma 0.00005562 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

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0Least InformativeDirect
Phenotypic Abnormality (PA)Neurodevelopmental abnormality0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of central motor function0.1649Moderately InformativeInherited
Phenotypic Abnormality (PA)Neurodevelopmental delay0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of coordination0.002255InformativeInherited
Phenotypic Abnormality (PA)Ataxia0.0007738Highly InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism environmental stimulus response variant0.00006212Least InformativeDirect
Worm Phenotype (WP)cell development variant0.00007089Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.0001434Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.0001907Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.007666Least InformativeInherited
Worm Phenotype (WP)organ system morphology variant0.01278Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.05569Least InformativeInherited
Worm Phenotype (WP)level of transgene expression variant0.00002612Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.0003062Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.00166Moderately InformativeInherited
Worm Phenotype (WP)feeding behavior variant0.001849Moderately InformativeInherited
Worm Phenotype (WP)early embryonic lethal0.01277Moderately InformativeInherited
Worm Phenotype (WP)cell component morphology variant0.1446Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.2532Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.2874Moderately InformativeInherited
Worm Phenotype (WP)transgene expression increased0.0000003843InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.00000726InformativeDirect
Worm Phenotype (WP)pleiotropic defects severe early emb0.000009357InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.00004056InformativeDirect
Worm Phenotype (WP)avoids bacterial lawn0.00005788InformativeDirect
Worm Phenotype (WP)endocytic transport defect0.002469InformativeInherited
Worm Phenotype (WP)RNA expression variant0.03293InformativeInherited
Worm Phenotype (WP)oocyte physiology variant0.03811InformativeInherited
Worm Phenotype (WP)germ cell cytoplasmic morphology variant0.07745InformativeInherited
Worm Phenotype (WP)oocyte morphology variant0.1129InformativeInherited
Worm Phenotype (WP)organelle organization biogenesis variant0.1933InformativeInherited
Worm Phenotype (WP)hypoxia resistant0Highly InformativeDirect
Worm Phenotype (WP)cell differentiation variant0.0000000000249Highly InformativeDirect
Worm Phenotype (WP)oocyte number decreased0.000008596Highly InformativeDirect
Worm Phenotype (WP)RNA processing variant0.0000173Highly InformativeDirect
Worm Phenotype (WP)nonsense mRNA accumulation0.0000793Highly InformativeDirect
Worm Phenotype (WP)cytoplasmic processing body variant0.0001503Highly InformativeDirect
Worm Phenotype (WP)level of protein expression variant0.0002132Highly InformativeDirect
Worm Phenotype (WP)nuclear appearance variant0.08354Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)nervous system0Least InformativeDirect
Zebrafish Anatomy (ZA)compound organ0Least InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)0 seed germination stage0.00003184InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Ligases forming aminoacyl-tRNA and related compounds0InformativeDirect
Enzyme Commission (EC)Valine--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Acid--ammonia (or amine) ligases (amide synthases)1Highly 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 functionMetal-binding0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Molecular functionRNA-binding1Moderately InformativeInherited
Molecular functiontRNA-binding0InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationAminoacyl-tRNA synthetase0InformativeDirect

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) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]