SUPERFAMILY 1.75 HMM library and genome assignments server


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 (3,197) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 9,170 61,186 4
Proteins 9,167 61,182 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) biosynthetic process 4.048e-13 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 1.269e-12 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 1.872e-12 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 9.273e-12 Least Informative Direct
Biological Process (BP) single-organism metabolic process 2.766e-11 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 7.781e-11 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 2.444e-09 Least Informative Direct
Biological Process (BP) protein metabolic process 2.8e-08 Least Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 8.577e-12 Moderately Informative Direct
Biological Process (BP) gene expression 9.186e-12 Moderately Informative Direct
Biological Process (BP) translation 0 Informative Direct
Biological Process (BP) ncRNA metabolic process 0 Informative Direct
Molecular Function (MF) binding 0.7145 Least Informative Inherited
Molecular Function (MF) anion binding 0.0274 Moderately Informative Inherited
Molecular Function (MF) purine ribonucleoside triphosphate binding 3.62e-08 Informative Direct
Molecular Function (MF) purine ribonucleoside binding 5.422e-08 Informative Direct
Molecular Function (MF) nucleotide binding 7.373e-07 Informative Direct
Molecular Function (MF) ATP binding 1.869e-09 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.0002774 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.1344 Least Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

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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

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)metabolism and growth0Least InformativeDirect
Yeast Phenotype (YP)vegetative growth0InformativeDirect

Document: YP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect

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)Acyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Ligases forming aminoacyl-tRNA and related compounds0InformativeDirect
Enzyme Commission (EC)Phenylalanine--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Valine--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Aminoacyltransferases0.2185Highly 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 functionATP-binding0Moderately InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationAminoacyl-tRNA synthetase0InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)tRNA modification0InformativeDirect
UniPathway (UP)aminoacyl-tRNA biosynthesis0Highly InformativeDirect

Document: UP 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) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]