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L9 N-domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   MbtH/L9 domain-like [ 55657] (2)
Superfamily:   L9 N-domain-like [ 55658] (2)
Families:   Ribosomal protein L9 N-domain [ 55659]
  N-terminal domain of RNase HI [ 55662]


Superfamily statistics
Genomes (3,019) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 4,302 21,309 12
Proteins 4,104 20,685 12


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 nitrogen compound metabolic process 0.001299 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.02582 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.02096 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.4844 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.1836 Least Informative Inherited
Biological Process (BP) amide biosynthetic process 0.000004299 Moderately Informative Direct
Biological Process (BP) peptide metabolic process 0.00000522 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.0003994 Moderately Informative Direct
Biological Process (BP) gene expression 0.01789 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity 0.00514 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.00000136 Moderately Informative Direct
Molecular Function (MF) nuclease activity 0.00000000001154 Informative Direct
Molecular Function (MF) endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomo 0 Highly Informative Direct
Molecular Function (MF) endoribonuclease activity 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.0003719 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.327 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.009986 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.07193 Least Informative Inherited
Cellular Component (CC) ribosome 0.000000007862 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.03899 Moderately Informative Inherited
Cellular Component (CC) large ribosomal subunit 0.0000000000002571 Informative Direct
Cellular Component (CC) mitochondrial ribosome 0.000005517 Informative Direct
Cellular Component (CC) mitochondrial large ribosomal subunit 0.0000002144 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)Acting on ester bonds0Least InformativeDirect
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters0Moderately InformativeDirect
Enzyme Commission (EC)Ribonuclease H0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranslation regulation0.000008207InformativeDirect
Cellular componentHost cytoplasm0.0000003334InformativeDirect
Post-translational modificationRNA-binding0Moderately InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationRibosomal protein0InformativeDirect
Post-translational modificationrRNA-binding0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009027 SSF55658 Protein matches
Abstract

The N-terminal domain of the ribosomal protein L9 is a regulatory RNA-binding module that binds to 23rRNA. L9 is composed of two domains and functions as a structural protein in the large subunit of the ribosome.

The N-terminal domain of eukaryotic RNase HI, which is lacking in retroviral and prokaryotic enzymes, shows a striking structural similarity to the L9 N-terminal domain, and may also function as a regulatory RNA-binding module. Eukaryotic RNases HI possess either one or two copies of the small N-terminal domain, in addition to the well-conserved catalytic RNase H domain. RNase HI belongs to the family of ribonuclease H enzymes that recognise RNA:DNA hybrids and degrade the RNA component.

The structures of both the L9 [PubMed8306963] and the RNase HI [PubMed10448044] N-terminal domains consist of a three-stranded antiparallel beta-sheet sandwiched between two short alpha-helices. The hydrophobic core of the domain is formed by the conserved residues that are involved in the packing of the alpha-helices onto the beta-sheet. The (beta)2/alpha/beta/alpha topology of the domain differs from the structures of known RNA binding domains such as the double-stranded RNA binding domain (dsRBD), the hnRNP K homology (KH) domain and the RNP motif.


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 L9 N-domain-like 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 L9 N-domain-like 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 ]