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tRNA-binding arm superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Long alpha-hairpin [ 46556] (20)
Superfamily:   tRNA-binding arm [ 46589] (4)
Families:   Seryl-tRNA synthetase (SerRS) [ 46590]
  Phenylalanyl-tRNA synthetase (PheRS) [ 46593]
  Valyl-tRNA synthetase (ValRS) C-terminal domain [ 81635]
  Methicillin resistance protein FemA probable tRNA-binding arm [ 81671]


Superfamily statistics
Genomes (3,203) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 9,194 50,880 4
Proteins 9,191 50,864 4


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) cellular aromatic compound metabolic process 0.000000000002502 Least Informative Direct
Biological Process (BP) biosynthetic 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) primary metabolic process 0.000000000004295 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.00000000000001422 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.00004633 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.000000000001728 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00000000001129 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) peptide metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.0008796 Moderately Informative Direct
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) amide biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.003902 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.005817 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.01048 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.005989 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.02492 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.01155 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.04336 Moderately Informative Inherited
Biological Process (BP) regulation of cytokine production 0.00000006439 Informative Direct
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.00005345 Informative Direct
Biological Process (BP) tRNA metabolic process 0 Informative Direct
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.0001121 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.0003552 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 0.00001319 Informative Direct
Biological Process (BP) negative regulation of cellular biosynthetic process 0.0001616 Informative Direct
Biological Process (BP) negative regulation of multicellular organismal process 0.00001372 Informative Direct
Biological Process (BP) negative regulation of cytokine production 0.0000000001211 Highly Informative Direct
Biological Process (BP) negative regulation of RNA metabolic process 0.000004533 Highly Informative Direct
Molecular Function (MF) binding 0.03885 Least Informative Inherited
Molecular Function (MF) small molecule binding 0.000323 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0.00004249 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.6144 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.08851 Moderately Informative Inherited
Molecular Function (MF) ligase activity 0 Informative Direct
Molecular Function (MF) purine nucleotide binding 0.0000002925 Informative Direct
Molecular Function (MF) ribonucleotide binding 0.0000003505 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.00000009992 Informative Direct
Molecular Function (MF) DNA binding 0.3217 Informative Inherited
Molecular Function (MF) double-stranded DNA binding 0.000001094 Highly Informative Direct
Molecular Function (MF) ATP binding 0.000000006495 Highly Informative Direct
Molecular Function (MF) sequence-specific DNA binding 0.00001406 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.000001874 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.641 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.09081 Least Informative Inherited

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)Phenylalanine--tRNA ligase0InformativeDirect
Enzyme Commission (EC)Aminoacyltransferases0.2514InformativeInherited
Enzyme Commission (EC)Valine--tRNA ligase0Highly InformativeDirect

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 functionMagnesium0Least InformativeDirect
Post-translational modificationAminoacyl-tRNA synthetase0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR010978 SSF46589 Protein matches
Abstract

This entry represents an alpha-helical tRNA-binding arm found in class I and II aminoacyl-tRNA synthetase enzymes, as well as in the methicillin resistance protein FemA.

The tRNA-binding arm domain is conserved between class I and class II aminoacyl-tRNA synthetase enzymes , consisting of two alpha helices in an antiparallel hairpin with a left-handed twist. The appended tRNA-binding domains recognize a small number of nucleotides that are conserved specifically in each cognate tRNA species for the discrimination between the cognate and noncognate tRNAs [PubMed12554880]. These nucleotides are called identity elements, and constitute the identity set. The tRNA-binding arm occurs as the C-terminal domain in some class I enzymes, such as valyl-tRNA synthetase, and as the N-terminal domain in some class II enzymes, such as phenylalanyl-tRNA synthetase.

The methicillin resistance protein, FemA (factors essential for methicillin resistance), contains a probable tRNA-binding arm that is similar in structure to those found in tRNA synthetases. In FemA, the tRNA-binding arm is inserted into the C-terminal NAT-like domain, and is thought to bind tRNA-glycine. FemA, along with FemB and FemX, plays a vital role in peptidoglycan biosynthesis specific to Staphylococci [PubMed12176388].


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 4 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 tRNA-binding arm 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 4 hidden Markov models representing the tRNA-binding arm 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 ]