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22  structures 4219  species 2  interactions 9872  sequences 31  architectures

Family: tRNA_edit (PF04073)

Summary: Aminoacyl-tRNA editing domain

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This is the Wikipedia entry entitled "YbaK protein domain". More...

YbaK protein domain Edit Wikipedia article

YbaK protein domain
PDB 1dbu EBI.jpg
Crystal structure of Cysteinyl-tRNA(Pro) deacylase protein from Haemophilus influenzae (hi1434)
Identifiers
Symbol YbaK
Pfam PF04073
InterPro IPR007214
SCOP 1dbx
SUPERFAMILY 1dbx

In molecular biology, this protein domain of unknown function is found in numerous prokaryote organisms. This domain also occurs in a number of prolyl-tRNA synthetases (proRS) from prokaryotes. Thus, the domain is thought to be involved in oligonucleotide binding, with possible roles in recognition/discrimination or editing of prolyl-tRNA.[1]

Function

Studies have shown that YbaK functions as a Cys-tRNAPro deacylase in vivo, deacetylation additionally involves turning genes off, hence, it can be assumed that it is preventing the addition of an amino acid to a tRNA molecule, thus preventing translation. In vitro studies with the full set of 20 E. coli aminoacyl-tRNAs revealed that the Haemophilus influenzae and E. coli YbaK proteins are moderately general aminoacyl-tRNA deacylases that preferentially hydrolyze Cys-tRNAPro and Cys-tRNACy. Furthermore, YbaK-mediated hydrolysis of aminoacyl-tRNA has been indicated to influence cell growth.[2] It has been further indicated that YbaK domain is important in the editing function if the wrong amino acid has been joined to the wrong tRNA.

Structure

The structure of YbaK shows a novel fold. This domain also occurs in a number of prolyl-tRNA synthetases (proRS) from prokaryotes. Thus, the domain is thought to be involved in oligonucleotide binding, with possible roles in recognition/discrimination or editing of prolyl-tRNA. YbaK is a highly curved mixed seven-stranded beta-sheet surrounded by six short alpha helices [1]


References

This article incorporates text from the public domain Pfam and InterPro IPR007214

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.

Aminoacyl-tRNA editing domain Provide feedback

This domain is found either on its own or in association with the tRNA synthetase class II core domain (PF00587). It is involved in the tRNA editing of mis-charged tRNAs including Cys-tRNA(Pro), Cys-tRNA(Cys), Ala-tRNA(Pro)[2-5]. The structure of this domain shows a novel fold [1].

Literature references

  1. Zhang H, Huang K, Li Z, Banerjei L, Fisher KE, Grishin NV, Eisenstein E, Herzberg O; , Proteins 2000;40:86-97.: Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8 A resolution: functional implications. PUBMED:10813833 EPMC:10813833

  2. Ruan B, Soll D;, J Biol Chem. 2005;280:25887-25891.: The bacterial YbaK protein is a Cys-tRNAPro and Cys-tRNA Cys deacylase. PUBMED:15886196 EPMC:15886196

  3. Ahel I, Korencic D, Ibba M, Soll D;, Proc Natl Acad Sci U S A. 2003;100:15422-15427.: Trans-editing of mischarged tRNAs. PUBMED:14663147 EPMC:14663147

  4. An S, Musier-Forsyth K;, J Biol Chem. 2005;280:34465-34472.: Cys-tRNA(Pro) editing by Haemophilus influenzae YbaK via a novel synthetase.YbaK.tRNA ternary complex. PUBMED:16087664 EPMC:16087664

  5. So BR, An S, Kumar S, Das M, Turner DA, Hadad CM, Musier-Forsyth K;, J Biol Chem. 2011;286:31810-31820.: Substrate-mediated fidelity mechanism ensures accurate decoding of proline codons. PUBMED:21768119 EPMC:21768119


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007214

This domain of unknown function is found in numerous prokaryote organisms. The structure of YbaK shows a novel fold. This domain also occurs in a number of prolyl-tRNA synthetases (proRS) from prokaryotes. Thus, the domain is thought to be involved in oligonucleotide binding, with possible roles in recognition/discrimination or editing of prolyl-tRNA [PUBMED:10813833].

Domain organisation

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

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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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(91)
Full
(9872)
Representative proteomes NCBI
(6622)
Meta
(1977)
RP15
(669)
RP35
(1310)
RP55
(1755)
RP75
(2098)
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Format an alignment

  Seed
(91)
Full
(9872)
Representative proteomes NCBI
(6622)
Meta
(1977)
RP15
(669)
RP35
(1310)
RP55
(1755)
RP75
(2098)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(91)
Full
(9872)
Representative proteomes NCBI
(6622)
Meta
(1977)
RP15
(669)
RP35
(1310)
RP55
(1755)
RP75
(2098)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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: manual;
Previous IDs: YbaK;
Type: Family
Author: Finn RD, Eberhardt R
Number in seed: 91
Number in full: 9872
Average length of the domain: 122.00 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 38.51 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.4 20.4
Trusted cut-off 20.4 20.4
Noise cut-off 20.3 20.2
Model length: 123
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

tRNA-synt_2b tRNA_edit

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 tRNA_edit 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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