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7  structures 4857  species 2  interactions 7484  sequences 22  architectures

Family: DALR_1 (PF05746)

Summary: DALR anticodon binding domain

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This is the Wikipedia entry entitled "Aminoacyl tRNA synthetase". More...

Aminoacyl tRNA synthetase Edit Wikipedia article

Anticodon-binding domain of tRNA
PDB 1obc EBI.jpg
leucyl-trna synthetase from thermus thermophilus complexed with a post-transfer editing substrate analogue
Identifiers
Symbol Anticodon_1
Pfam PF08264
InterPro IPR013155
SCOP 1ivs
SUPERFAMILY 1ivs
DALR anticodon binding domain 1
PDB 1iq0 EBI.jpg
thermus thermophilus arginyl-trna synthetase
Identifiers
Symbol DALR_1
Pfam PF05746
Pfam clan CL0258
InterPro IPR008909
SCOP 1bs2
SUPERFAMILY 1bs2
DALR anticodon binding domain 2
PDB 1u0b EBI.jpg
crystal structure of cysteinyl-trna synthetase binary complex with trnacys
Identifiers
Symbol DALR_2
Pfam PF09190
Pfam clan CL0258
InterPro IPR015273

An aminoacyl tRNA synthetase (aaRS) is an enzyme that catalyzes the esterification of a specific amino acid or its precursor to one of all its compatible cognate tRNAs to form an aminoacyl-tRNA. In other words, aminoacyl tRNA synthetase simply attaches the appropriate, or "cognate," amino acid onto the corresponding tRNA. This is sometimes called "charging" or "loading" the tRNA with the amino acid. Once the tRNA is charged, a ribosome can transfer the amino acid from the tRNA onto a growing peptide, according to the genetic code.

Mechanism[edit]

The synthetase first binds ATP and the corresponding amino acid or its precursor to form an aminoacyl-adenylate and release inorganic pyrophosphate (PPi). The adenylate-aaRS complex then binds the appropriate tRNA molecule, and the amino acid is transferred from the aa-AMP to either the 2'- or the 3'-OH of the last tRNA nucleotide (A76) at the 3'-end. Some synthetases also mediate a proofreading reaction to ensure high fidelity of tRNA charging; if the tRNA is found to be improperly charged, the aminoacyl-tRNA bond is hydrolyzed.

Reaction[edit]

Reaction:

  1. amino acid + ATP → aminoacyl-AMP + PPi
  2. aminoacyl-AMP + tRNA → aminoacyl-tRNA + AMP

Sum of 1 and 2: amino acid + tRNA + ATP → aminoacyl-tRNA + AMP + PPi

Classes[edit]

There are two classes of aminoacyl tRNA synthetase:[1]

The amino acids are attached to the hydroxyl (-OH) group of the adenosine via the carboxyl (-COOH) group.

Regardless of where the aminoacyl is initially attached to the nucleotide, the 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.

Structures[edit]

Both classes of aminoacyl-tRNA synthetases are multidomain proteins. In a typical scenario, an aaRS consists of a catalytic domain (where both the above reactions take place) and an anticodon binding domain (which interacts mostly with the anticodon region of the tRNA and ensures binding of the correct tRNA to the amino acid). In addition, some aaRSs have additional RNA binding domains and editing domains[2] that cleave incorrectly paired aminoacyl-tRNA molecules.

The catalytic domains of all the aaRSs of a given class are found to be homologous to one another, whereas class I and class II aaRSs are unrelated to one another. The class I aaRSs have the ubiquitous Rossmann fold and have the parallel beta-strands architecture, whereas the class II aaRSs have a unique fold made up of antiparallel beta-strands.

The alpha helical anticodon binding domain of Arginyl, Glycyl and Cysteinyl-tRNA synthetases is known as the DALR domain after characteristic conserved amino acids.[3]

Evolution[edit]

Most of the aaRSs of a given specificity are evolutionarily closer to one another than to aaRSs of another specificity. However, AsnRS and GlnRS group within AspRS and GluRS, respectively. Most of the aaRSs of a given specificity also belong to a single class. However, there are two distinct versions of the LysRS - one belonging to the class I family and the other belonging to the class II family.

In addition, the molecular phylogenies of aaRSs are often not consistent with accepted organismal phylogenies, e.g. they violate the so-called canonical phylogenetic pattern shown by most other enzymes for the three domains of life - Archaea, Bacteria, and Eukarya. Furthermore, the phylogenies inferred for aaRSs of different amino acids often do not agree with one another. These are two clear indications that horizontal transfer has occurred several times during the evolutionary history of aaRSs.[4]

Expanding the genetic code via mutant aminoacyl tRNA synthetases[edit]

In some of the aminoacyl tRNA synthetases, the cavity that holds the amino acid can be mutated and modified to carry artificial, unnatural amino acids synthesized in the lab, and to attach them to specific tRNAs. This expands the genetic code, beyond the twenty amino acids universal in nature, to include an unnatural amino acid as well. The unnatural amino acid is coded by an otherwise non-coding base triplet such as the amber stop codon. The organism that expresses the mutant synthetase can then be genetically programmed to incorporate the unnatural amino acid into any desired position in any protein of interest, allowing biochemists or structural biologists to probe or change the protein's function. For instance, one can start with the gene for a protein that binds a certain sequence of DNA, and, by directing an unnatural amino acid with a reactive side-chain into the binding site, create a new protein that cuts the DNA at the target-sequence, rather than binding it.

By mutating aminoacyl tRNA synthetases, chemists have expanded the genetic codes of various organisms to include lab-synthesized amino acids with all kinds of useful properties: photoreactive, metal-chelating, xenon-chelating, crosslinking, color-changing, spin-resonant, fluorescent, biotinylated, and redox-active amino acids.[5]

Prediction Servers[edit]

See also[edit]

References[edit]

  1. ^ "tRNA Synthetases". Retrieved 2007-08-18. 
  2. ^ "Molecule of the Month: Aminoacyl-tRNA Synthetases High Fidelity". Retrieved 2013-08-04. 
  3. ^ Wolf YI, Aravind L, Grishin NV, Koonin EV (August 1999). "Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events". Genome Res. 9 (8): 689–710. doi:10.1101/gr.9.8.689. PMID 10447505. 
  4. ^ Woese, CR; Olsen, GJ; Ibba, M; Söll, D (March 2000). "Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process.". Microbiology and molecular biology reviews : MMBR 64 (1): 202–36. doi:10.1128/MMBR.64.1.202-236.2000. PMID 10704480. 
  5. ^ Peter G. Schultz, Expanding the genetic code

External links[edit]

This article incorporates text from the public domain Pfam and InterPro IPR015273

This article incorporates text from the public domain Pfam and InterPro IPR008909

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.

DALR anticodon binding domain Provide feedback

This all alpha helical domain is the anticodon binding domain in Arginyl and glycyl tRNA synthetase. This domain is known as the DALR domain after characteristic conserved amino acids [1].

Literature references

  1. Wolf YI, Aravind L, Grishin NV, Koonin EV; , Genome Res 1999;9:689-710.: Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. PUBMED:10447505 EPMC:10447505


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008909

The aminoacyl-tRNA synthetases (EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology [PUBMED:2203971]. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric [PUBMED:10673435]. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [PUBMED:8364025], and are mostly dimeric or multimeric, containing at least three conserved regions [PUBMED:8274143, PUBMED:2053131, PUBMED:1852601]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases [PUBMED:]. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c.

This all alpha helical domain is the anticodon binding domain of Arginyl tRNA synthetase. This domain is known as the DALR domain after characteristic conserved amino acids [PUBMED:10447505].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 DALR (CL0258), which contains the following 2 members:

DALR_1 DALR_2

Alignments

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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
(104)
Full
(7484)
Representative proteomes NCBI
(5803)
Meta
(2941)
RP15
(661)
RP35
(1256)
RP55
(1662)
RP75
(2023)
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  Seed
(104)
Full
(7484)
Representative proteomes NCBI
(5803)
Meta
(2941)
RP15
(661)
RP35
(1256)
RP55
(1662)
RP75
(2023)
Alignment:
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Sequence:
Gaps:
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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
(104)
Full
(7484)
Representative proteomes NCBI
(5803)
Meta
(2941)
RP15
(661)
RP35
(1256)
RP55
(1662)
RP75
(2023)
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.

Pfam alignments:

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_196 (release 8.0)
Previous IDs: tRNA-synt_1d_C;
Type: Domain
Author: Bateman A
Number in seed: 104
Number in full: 7484
Average length of the domain: 115.90 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 19.29 %

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 22.3 22.3
Trusted cut-off 22.3 22.3
Noise cut-off 22.2 22.2
Model length: 119
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...

Arg_tRNA_synt_N tRNA-synt_1d

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 DALR_1 domain has been found. There are 7 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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