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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 (3,012) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 4,284 18,824 12
Proteins 4,087 18,547 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 0.0001732 Least Informative Direct
Biological Process (BP) biosynthetic process 0.004558 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.004887 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.005242 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.2313 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.05803 Least Informative Inherited
Biological Process (BP) peptide metabolic process 0.00000022 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.0001213 Moderately Informative Direct
Biological Process (BP) amide biosynthetic process 0.0000001608 Moderately Informative Direct
Biological Process (BP) organelle organization 0.03132 Moderately Informative Inherited
Biological Process (BP) gene expression 0.007635 Moderately Informative Inherited
Biological Process (BP) mitochondrion organization 0.000004591 Informative Direct
Molecular Function (MF) hydrolase activity 0.003064 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.0000007454 Moderately Informative Direct
Molecular Function (MF) nuclease activity 0.000000000006192 Informative Direct
Molecular Function (MF) endoribonuclease activity 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.0001729 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.2269 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.0627 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.01195 Least Informative Inherited
Cellular Component (CC) ribosome 0.000000005925 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 0.0004049 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.02019 Moderately Informative Inherited
Cellular Component (CC) organellar large ribosomal subunit 0.00052 Informative Direct
Cellular Component (CC) mitochondrial ribosome 0.00001772 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

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranslation regulation0.00000721InformativeDirect
Cellular componentHost cytoplasm0.0000001348InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionrRNA-binding0InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationRibosomal protein0InformativeDirect

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) · Arabidopsis Plant Ontology (AP) · 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) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]