Summary: Peptidyl-tRNA hydrolase PTH2
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Peptidyl-tRNA hydrolase PTH2 Provide feedback
Peptidyl-tRNA hydrolases are enzymes that release tRNAs from peptidyl-tRNA during translation.
Rosas-Sandoval G, Ambrogelly A, Rinehart J, Wei D, Cruz-Vera LR, Graham DE, Stetter KO, Guarneros G, Soll D; , Proc Natl Acad Sci U S A 2002;99:16707-16712.: Orthologs of a novel archaeal and of the bacterial peptidyl-tRNA hydrolase are nonessential in yeast. PUBMED:12475929 EPMC:12475929
Internal database links
|Similarity to PfamA using HHSearch:||DUF2000|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR002833Peptidyl-tRNA hydrolases are enzymes that release tRNAs from peptidyl-tRNA during translation.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||aminoacyl-tRNA hydrolase activity (GO:0004045)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
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This clan includes Peptidyl-tRNA hydrolase II as well as a large family of uncharacterised proteins called DUF2000. A structure for DUF2000 shows a similar structure to PTH2. It is not clear if the DUF2000 family are also Peptidyl-tRNA hydrolases. Both families contain a conserved positively charged residue close to the amino terminus that may be part of the active site.
The clan contains the following 2 members:DUF2000 PTH2
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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Curation and family details
|Seed source:||Enright A|
|Previous IDs:||DUF119;UPF0099; Pep-tRNA_hydrol;|
|Author:||Enright A, Ouzounis C, Bateman A, Mistry J, Wood V|
|Number in seed:||69|
|Number in full:||1006|
|Average length of the domain:||109.50 aa|
|Average identity of full alignment:||31 %|
|Average coverage of the sequence by the domain:||60.74 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||11|
|Download:||download the raw HMM for this family|
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 PTH2 domain has been found. There are 22 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 seqence.
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