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mRNA decapping enzyme DcpS N-terminal domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   mRNA decapping enzyme DcpS N-terminal domain [ 102859]
Superfamily:   mRNA decapping enzyme DcpS N-terminal domain [ 102860]
Families:   mRNA decapping enzyme DcpS N-terminal domain [ 102861]


Superfamily statistics
Genomes (355) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 402 517 5
Proteins 401 514 5


Functional annotation
General category Other
Detailed category Unknown function

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) heterocycle metabolic process 0.0000000004541 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.0000000005516 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000000001262 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.000000003854 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.00000002247 Least Informative Direct
Biological Process (BP) response to stimulus 0.0001858 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.4679 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.002781 Least Informative Inherited
Biological Process (BP) RNA metabolic process 0.00000000000004447 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.02991 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.02763 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.001065 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.2612 Moderately Informative Inherited
Biological Process (BP) gene expression 0.06795 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.002352 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.004291 Moderately Informative Inherited
Biological Process (BP) negative regulation of cell death 0.00000004654 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.00004899 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.001576 Informative Inherited
Biological Process (BP) RNA processing 0.2245 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.003515 Informative Inherited
Biological Process (BP) RNA splicing 0.00000000098 Highly Informative Direct
Biological Process (BP) mRNA catabolic process 0.01455 Highly Informative Inherited
Biological Process (BP) mRNA processing 0.1868 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.00000000001818 Least Informative Direct
Molecular Function (MF) binding 0.00001309 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0.00000000005328 Moderately Informative Direct
Molecular Function (MF) RNA binding 0.000000000000001562 Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.822 Least Informative Inherited

Document: GO 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)Acting on acid anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)In phosphorous-containing anhydrides0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processmRNA splicing0.000000000001112InformativeDirect
Cellular componentNucleus0.0000001012Least InformativeDirect
Post-translational modificationHydrolase0.000000006605Least InformativeDirect
Post-translational modificationAcetylation0.000009714Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011145 SSF102860 Protein matches
Abstract

This entry represents the N-terminal domain of scavenger mRNA decapping enzymes, such as Dcp2 and DcpS. DcpS is a scavenger pyrophosphatase that hydrolyses the residual cap structure following 3' to 5' mRNA degradation. DcpS uses cap dinucleotides or capped oligonucleotides as substrate to release m(7)GMP (N7-methyl GMP), while Dcp2 uses capped mRNA as substrate in order to hydrolyse the cap to release m(7)GDP (N7-methyl GDP) [PubMed16246173]. The association of DcpS with 3' to 5' exonuclease exosome components suggests that these two activities are linked and there is a coupled exonucleolytic decay-dependent decapping pathway. The family contains a histidine triad (HIT) sequence with three histidines separated by hydrophobic residues [PubMed16001405]. The central histidine within the DcpS HIT motif is critical for decapping activity and defines the HIT motif as a new mRNA decapping domain, making DcpS the first member of the HIT family of proteins with a defined biological function. This family is related to

More information about these proteins can be found at Protein of the Month: RNA Exosomes.


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 2 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 mRNA decapping enzyme DcpS N-terminal 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 2 hidden Markov models representing the mRNA decapping enzyme DcpS N-terminal 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-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]