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Translation proteins SH3-like domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   SH3-like barrel [ 50036] (21)
Superfamily:   Translation proteins SH3-like domain [ 50104] (7)
Families:   Ribosomal proteins L24p and L21e [ 50105] (2)
  eIF5a N-terminal domain-like [ 50110] (3)
  C-terminal domain of ribosomal protein L2 [ 50114]
  N-utilization substance G protein NusG, C-terminal domain [ 82072]
  SPT5 KOW domain-like [ 141242]
  Ribosomal protein L19 [ 141245]
  Ribosomal protein L14e [ 159031]


Superfamily statistics
Genomes (3,262) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 24,080 115,984 46
Proteins 23,915 115,625 46


Functional annotation
General category Information
Detailed category Translation

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)cellular nitrogen compound metabolic process0.00000071230Least InformativeDirect
Biological Process (BP)macromolecule metabolic process0.0000036390Least InformativeDirect
Biological Process (BP)biosynthetic process0.000050410Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.0000094560.01893Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.0073450.000000253Least InformativeInherited
Biological Process (BP)primary metabolic process0.002880.0000000002366Least InformativeInherited
Biological Process (BP)peptide metabolic process00Moderately InformativeDirect
Biological Process (BP)amide biosynthetic process0.000000000000006150Moderately InformativeDirect
Biological Process (BP)gene expression0.000000000000075440Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.0000000010270Moderately InformativeDirect
Biological Process (BP)macromolecular complex subunit organization0.00000029590.000000008173Moderately InformativeDirect
Biological Process (BP)cellular component assembly0.042490.007055Moderately InformativeInherited
Biological Process (BP)organelle organization0.000010360.008895Moderately InformativeInherited
Biological Process (BP)ribosome biogenesis00InformativeDirect
Biological Process (BP)ribonucleoprotein complex subunit organization0.000000000000026290.0000000000003352InformativeDirect
Biological Process (BP)organelle assembly0.000000000045160.000000000001693InformativeDirect
Biological Process (BP)ribosome assembly0.00014660.00000000000003269Highly InformativeDirect
Molecular Function (MF)binding0.51951Least InformativeInherited
Molecular Function (MF)structural molecule activity00Moderately InformativeDirect
Molecular Function (MF)nucleic acid binding0.0000043580.00001006Moderately InformativeDirect
Molecular Function (MF)RNA binding0.000000072760.00000000001192InformativeDirect
Cellular Component (CC)non-membrane-bounded organelle0.000000000025880Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.000001670Least InformativeDirect
Cellular Component (CC)cytoplasmic part0.00049590.0000000000006468Least InformativeDirect
Cellular Component (CC)ribosome00Moderately InformativeDirect
Cellular Component (CC)cytosolic part00Moderately InformativeDirect
Cellular Component (CC)large ribosomal subunit00InformativeDirect
Cellular Component (CC)cytosolic ribosome00.000001491InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
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) biosynthetic process 0 Least Informative Direct
Biological Process (BP) primary metabolic process 0.0000000002366 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.000000253 Least Informative Direct
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.01893 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) peptide metabolic process 0 Moderately Informative Direct
Biological Process (BP) amide biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.000000008173 Moderately Informative Direct
Biological Process (BP) cellular component assembly 0.007055 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.008895 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.4709 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.5382 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.65 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 1 Moderately Informative Inherited
Biological Process (BP) ribosome biogenesis 0 Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 0.0000000000003352 Informative Direct
Biological Process (BP) organelle assembly 0.000000000001693 Informative Direct
Biological Process (BP) ribosome assembly 0.00000000000003269 Highly Informative Direct
Biological Process (BP) translational initiation 0.0000004007 Highly Informative Direct
Biological Process (BP) mitochondrial gene expression 0.000121 Highly Informative Direct
Biological Process (BP) rRNA metabolic process 0.0008815 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) structural molecule activity 0 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.00001006 Moderately Informative Direct
Molecular Function (MF) RNA binding 0.00000000001192 Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.0000000000006468 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) ribosome 0 Moderately Informative Direct
Cellular Component (CC) cytosolic part 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.00005065 Moderately Informative Direct
Cellular Component (CC) nuclear part 1 Moderately Informative Inherited
Cellular Component (CC) large ribosomal subunit 0 Informative Direct
Cellular Component (CC) cytosolic ribosome 0.000001491 Informative Direct
Cellular Component (CC) mitochondrial ribosome 0 Informative Direct
Cellular Component (CC) nucleoplasm part 0.01122 Informative Inherited
Cellular Component (CC) plastid 0.001924 Informative Inherited
Cellular Component (CC) mitochondrial large ribosomal subunit 0 Highly Informative Direct
Cellular Component (CC) transcription elongation factor complex 0.00000000000002553 Highly Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation1Moderately InformativeInherited
Biological processProtein biosynthesis0InformativeDirect
Biological processTranscription termination0Highly InformativeDirect
Cellular componentPlastid0.000000000000001304Moderately InformativeDirect
Post-translational modificationRNA-binding0Moderately InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationRibosomal protein0InformativeDirect
Post-translational modificationInitiation factor0InformativeDirect
Post-translational modificationrRNA-binding0InformativeDirect
Post-translational modificationElongation factor0Highly InformativeDirect
Post-translational modificationHydroxylation0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008991 SSF50104 Protein matches
Abstract

The fundamental activity of the ribosome is two-fold: to decode the message of the mRNA in the small subunit, and to form a peptide bond between peptidyl-tRNA and aminoacyl-tRNA by a peptidyl transferase activity in the large subunit. Several prokaryotic and eukaryotic proteins that are involved in the translation process contain an SH3-like domain. The structure of the translation protein SH3-like domain is a partly opened beta barrel, where the last strand is interrupted by a 3-10 helical turn. The structure of the RNA-binding C-terminal domain of the Bacillus stearothermophilus ribosomal protein L2 has been shown to adopt the SH3-like barrel topology [PubMed10075918]. The L2 protein is located near the peptidyl transferase centre in the large ribosomal subunit where it may contribute to peptidyl transferase activity, and is involved in the assembly of the 23SrRNA. Likewise, the N-terminal domain of the ubiquitous eukaryotic initiation translation factor 5a (IF-5A) protein adopts the SH3-like barrel topology [PubMed9724718, PubMed9753699]. IF-5A is involved in the initial step of peptide bond formation in translation and in cell-cycle regulation. IF-5A acts as a cofactor of the Rev protein in HIV-1-infected cells and of the Rex protein in T-cell leukaemia virus 1-infected cells.


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-quality) · Gene Ontology (high-coverage) · 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 23 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 Translation proteins SH3-like domain 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 23 hidden Markov models representing the Translation proteins SH3-like domain 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-quality) · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) · Internal database links ]