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32  structures 6683  species 0  interactions 16426  sequences 85  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)

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]


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.


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]


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

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007214

Bacterial prolyl-tRNA synthetases and some smaller paralogues, YbaK and ProX, can hydrolyse misacylated Cys-tRNA(Pro) or Ala-tRNA(Pro) [ PUBMED:15886196 ]. The small bacterial protein Ybak preferentially hydrolyses Cys-tRNA(Pro) and Cys-tRNA(Cys) [ PUBMED:15886196 , PUBMED:23185990 ]. ProX functions in trans to edit the amino acid moiety from incorrectly charged Ala-tRNA(Pro) [ PUBMED:14663147 ]. Prolyl-tRNA synthetases main function is to catalyse the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro) [ PUBMED:10642548 ].

This entry represents a domain characteristic of Ybak and ProX, that can also be found with other domains in prolyl-tRNA synthetases.

Gene Ontology

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Domain organisation

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Seed source: manual;
Previous IDs: YbaK;
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Eberhardt R
Number in seed: 63
Number in full: 16426
Average length of the domain: 123.00 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 40.55 %

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 25.5 25.5
Trusted cut-off 25.5 25.5
Noise cut-off 25.4 25.4
Model length: 123
Family (HMM) version: 17
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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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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 32 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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