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64  structures 1464  species 0  interactions 3797  sequences 109  architectures

Family: DcpS_C (PF11969)

Summary: Scavenger mRNA decapping enzyme C-term binding

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This is the Wikipedia entry entitled "DCPS (gene)". More...

DCPS (gene) Edit Wikipedia article

DCPS
Protein DCPS PDB 1st0.png
Available structures
PDBOrtholog search: PDBe RCSB
Identifiers
AliasesDCPS, DCS1, HINT-5, HINT5, HSL1, ARS, HSPC015, decapping enzyme, scavenger
External IDsOMIM: 610534 MGI: 1916555 HomoloGene: 32202 GeneCards: DCPS
Gene location (Human)
Chromosome 11 (human)
Chr.Chromosome 11 (human)[1]
Chromosome 11 (human)
Genomic location for DCPS
Genomic location for DCPS
Band11q24.2Start126,304,060 bp[1]
End126,350,005 bp[1]
Orthologs
SpeciesHumanMouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_014026
NM_001350236

NM_027030

RefSeq (protein)

NP_054745
NP_001337165

NP_081306

Location (UCSC)Chr 11: 126.3 – 126.35 MbChr 9: 35.12 – 35.18 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse
Scavenger mRNA decapping enzyme (DcpS) N-terminal
PDB 1vlr EBI.jpg
crystal structure of mrna decapping enzyme (dcps) from mus musculus at 1.83 a resolution
Identifiers
SymbolDcpS
PfamPF05652
InterProIPR008594
SCOPe1st4 / SUPFAM
Scavenger mRNA decapping enzyme C-term binding
Identifiers
SymbolDcpS_C
PfamPF11969
Pfam clanCL0265
SCOPe1st4 / SUPFAM

Scavenger mRNA-decapping enzyme DcpS is a protein that in humans is encoded by the DCPS gene.[5][6][7]

The scavenger mRNA decapping enzymes include 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 substrates to release m(7)GMP (N7-methyl GMP), while Dcp2 uses capped mRNA as a substrate in order to hydrolyse the cap to release m(7)GDP (N7-methyl GDP).[8] 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 in its C-terminal domain, with three histidines separated by hydrophobic residues.[9] 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.


References

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000110063 - Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000032040 - Ensembl, May 2017
  3. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ^ Liu H, Rodgers ND, Jiao X, Kiledjian M (Aug 2002). "The scavenger mRNA decapping enzyme DcpS is a member of the HIT family of pyrophosphatases". EMBO J. 21 (17): 4699–4708. doi:10.1093/emboj/cdf448. PMC 126188. PMID 12198172.
  6. ^ van Dijk E, Le Hir H, Seraphin B (Oct 2003). "DcpS can act in the 5'-3' mRNA decay pathway in addition to the 3'-5' pathway". Proc Natl Acad Sci U S A. 100 (21): 12081–12086. doi:10.1073/pnas.1635192100. PMC 218716. PMID 14523240.
  7. ^ "Entrez Gene: DCPS decapping enzyme, scavenger".
  8. ^ Liu H, Kiledjian M (February 2006). "Decapping the message: a beginning or an end". Biochem. Soc. Trans. 34 (Pt 1): 35–8. doi:10.1042/BST20060035. PMID 16246173.
  9. ^ Han GW, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Axelrod H, Biorac T, Canaves JM, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Haugen J, Hornsby M, Jaroszewski L, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, McPhillips TM, Miller MD, Moy K, Nigoghossian E, Paulsen J, Quijano K, Reyes R, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA (September 2005). "Crystal structure of an Apo mRNA decapping enzyme (DcpS) from Mouse at 1.83 A resolution". Proteins. 60 (4): 797–802. doi:10.1002/prot.20467. PMID 16001405.

See also

Further reading

External links

  • PDBe-KB provides an overview of all the structure information available in the PDB for Human m7GpppX diphosphatase (DCPS)


This article incorporates text from the public domain Pfam and InterPro: IPR008594


This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Scavenger mRNA decapping enzyme C-term binding Provide feedback

This family consists of several scavenger mRNA decapping enzymes (DcpS) and is the C-terminal region. DcpS is a scavenger pyrophosphatase that hydrolyses the residual cap structure following 3' to 5' decay of an mRNA. 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 C-terminal domain contains a histidine triad (HIT) sequence with three histidines separated by hydrophobic residues. 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.

Literature references

  1. Liu H, Rodgers ND, Jiao X, Kiledjian M; , EMBO J 2002;21:4699-4708.: The scavenger mRNA decapping enzyme DcpS is a member of the HIT family of pyrophosphatases. PUBMED:12198172 EPMC:12198172


Internal database links

External database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan HIT (CL0265), which has the following description:

The HIT superfamily are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides [1].

The clan contains the following 11 members:

Ap4A_phos_N ATP_transf CDH CwfJ_C_1 DcpS_C DUF4921 DUF4922 DUF4931 GalP_UDP_tr_C GalP_UDP_transf HIT

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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  Seed
(66)
Full
(3797)
Representative proteomes UniProt
(7377)
RP15
(805)
RP35
(1821)
RP55
(3082)
RP75
(4073)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

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  Seed
(66)
Full
(3797)
Representative proteomes UniProt
(7377)
RP15
(805)
RP35
(1821)
RP55
(3082)
RP75
(4073)
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(66)
Full
(3797)
Representative proteomes UniProt
(7377)
RP15
(805)
RP35
(1821)
RP55
(3082)
RP75
(4073)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_9894 (release 8.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Moxon SJ
Number in seed: 66
Number in full: 3797
Average length of the domain: 115.40 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 38.30 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.9 20.9
Trusted cut-off 20.9 20.9
Noise cut-off 20.8 20.8
Model length: 114
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the DcpS_C domain has been found. There are 64 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0P0VWB2 View 3D Structure Click here
A0A0R0EB75 View 3D Structure Click here
A0A0R0GF78 View 3D Structure Click here
A0A1D6JB03 View 3D Structure Click here
A0A1D6JZE9 View 3D Structure Click here
A0A1D8PQS6 View 3D Structure Click here
A0A1D8PSG1 View 3D Structure Click here
A0A1D8PSI5 View 3D Structure Click here
A4I4B7 View 3D Structure Click here
C6TCG0 View 3D Structure Click here
D3KFR7 View 3D Structure Click here
E7F132 View 3D Structure Click here
F1R776 View 3D Structure Click here
G5EFS4 View 3D Structure Click here
K7K399 View 3D Structure Click here
P61799 View 3D Structure Click here
Q06151 View 3D Structure Click here
Q0JBF2 View 3D Structure Click here
Q12123 View 3D Structure Click here
Q4DHQ5 View 3D Structure Click here
Q4DWA1 View 3D Structure Click here
Q4DXF4 View 3D Structure Click here
Q54DF5 View 3D Structure Click here
Q558W0 View 3D Structure Click here
Q5PNN8 View 3D Structure Click here
Q6IIA4 View 3D Structure Click here
Q7TQC5 View 3D Structure Click here
Q7Z2E3 View 3D Structure Click here
Q84VV6 View 3D Structure Click here
Q8GYJ9 View 3D Structure Click here
Q8K3P7 View 3D Structure Click here
Q8K4F7 View 3D Structure Click here
Q8K4H4 View 3D Structure Click here
Q8MSG8 View 3D Structure Click here
Q8MSG8 View 3D Structure Click here
Q96C86 View 3D Structure Click here
Q9CPS6 View 3D Structure Click here
Q9DAR7 View 3D Structure Click here
Q9M041 View 3D Structure Click here
Q9NQE9 View 3D Structure Click here
Q9P7C9 View 3D Structure Click here
Q9VNH5 View 3D Structure Click here
Q9VQ59 View 3D Structure Click here