SUPERFAMILY 1.75 HMM library and genome assignments server


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 2.052e-09 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 2.498e-09 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 5.626e-09 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 1.673e-08 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 1.012e-07 Least Informative Direct
Biological Process (BP) response to stimulus 0.0004847 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.47 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.004905 Least Informative Inherited
Biological Process (BP) RNA metabolic process 2.346e-13 Moderately Informative Direct
Biological Process (BP) regulation of programmed cell death 2.119e-06 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.02905 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.02607 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.001008 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.256 Moderately Informative Inherited
Biological Process (BP) gene expression 0.06812 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.00233 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound catabolic process 0.001102 Moderately Informative Inherited
Biological Process (BP) negative regulation of cell death 7.126e-08 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 4.828e-05 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.001541 Informative Inherited
Biological Process (BP) RNA processing 0.2242 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.003443 Informative Inherited
Biological Process (BP) RNA splicing 1.613e-09 Highly Informative Direct
Biological Process (BP) mRNA catabolic process 0.01455 Highly Informative Inherited
Biological Process (BP) mRNA processing 0.1837 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 8.882e-11 Least Informative Direct
Molecular Function (MF) binding 0.0001191 Least Informative Direct
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 1.772e-10 Moderately Informative Direct
Molecular Function (MF) RNA binding 7.537e-15 Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.8247 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 splicing1.094e-12InformativeDirect
Cellular componentNucleus9.988e-08Least InformativeDirect
Post-translational modificationHydrolase6.41e-09Least InformativeDirect
Post-translational modificationAcetylation9.693e-06Least 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 ]