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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 2018_03 genome PDB chains (SCOP 1.75)
Domains 23,726 167,420 14
Proteins 23,281 164,437 14


Functional annotation
General category Information
Detailed category Translation

Document:
Function annotation of SCOP domain superfamilies

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 nervous system physiology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the digestive system0.009975Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.2686Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0.0006014Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of digestive system physiology0.0006204Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.6039Moderately InformativeInherited
Phenotypic Abnormality (PA)Hepatic steatosis0.00006731InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell development variant0.00008635Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.0001797Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.0002883Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.002119Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.01073Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.05992Least InformativeInherited
Worm Phenotype (WP)organ system morphology variant0.07212Least InformativeInherited
Worm Phenotype (WP)level of transgene expression variant0.00004256Moderately InformativeDirect
Worm Phenotype (WP)cell component morphology variant0.0002792Moderately InformativeDirect
Worm Phenotype (WP)feeding behavior variant0.001881Moderately InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.003076Moderately InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.01192Moderately InformativeInherited
Worm Phenotype (WP)early embryonic lethal0.01304Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.2579Moderately InformativeInherited
Worm Phenotype (WP)protein expression variant0.2655Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.5592Moderately InformativeInherited
Worm Phenotype (WP)oxygen response variant0.000000007767InformativeDirect
Worm Phenotype (WP)transgene expression increased0.0000007099InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.000007316InformativeDirect
Worm Phenotype (WP)pleiotropic defects severe early emb0.000009634InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.00004051InformativeDirect
Worm Phenotype (WP)rachis morphology variant0.00004235InformativeDirect
Worm Phenotype (WP)avoids bacterial lawn0.00005782InformativeDirect
Worm Phenotype (WP)oocyte morphology variant0.000261InformativeDirect
Worm Phenotype (WP)level of protein expression variant0.001154InformativeInherited
Worm Phenotype (WP)endocytic transport defect0.002557InformativeInherited
Worm Phenotype (WP)oocyte physiology variant0.03069InformativeInherited
Worm Phenotype (WP)organelle organization biogenesis variant0.2211InformativeInherited
Worm Phenotype (WP)organism pathogen response variant0.2507InformativeInherited
Worm Phenotype (WP)hypoxia resistant0Highly InformativeDirect
Worm Phenotype (WP)cell differentiation variant0.00000000004201Highly InformativeDirect
Worm Phenotype (WP)pachytene region organization variant0.000004217Highly InformativeDirect
Worm Phenotype (WP)oocyte number decreased0.000008666Highly InformativeDirect
Worm Phenotype (WP)protein expression reduced0.0004137Highly InformativeDirect
Worm Phenotype (WP)nuclear appearance variant0.08203Highly 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

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)larva0Least InformativeDirect

Document: FA 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)Acid--ammonia (or amine) ligases (amide synthases)1Highly InformativeInherited

Document: EC 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 · Enzyme Commission (EC) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) ]

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