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28  structures 8104  species 0  interactions 10406  sequences 75  architectures

Family: Arg_tRNA_synt_N (PF03485)

Summary: Arginyl tRNA synthetase N terminal domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Arginine-tRNA ligase". More...

Arginine-tRNA ligase Edit Wikipedia article

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

This is the Wikipedia entry entitled "Arginine—tRNA ligase". More...

Arginine—tRNA ligase Edit Wikipedia article

arginine-tRNA ligase
Identifiers
EC no.6.1.1.19
CAS no.37205-35-9
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structuresRCSB PDB PDBe PDBsum
Gene OntologyAmiGO / QuickGO
Arginyl tRNA synthetase N terminal domain
PDB 1bs2 EBI.jpg
yeast arginyl-trna synthetase
Identifiers
SymbolArg_tRNA_synt_N
PfamPF03485
InterProIPR005148
SCOP21f7u / SCOPe / SUPFAM

In enzymology, an arginine-tRNA ligase (EC 6.1.1.19) is an enzyme that catalyzes the chemical reaction

ATP + L-arginine + tRNAArg AMP + diphosphate + L-arginyl-tRNAArg

The 3 substrates of this enzyme are ATP, L-arginine, and tRNA(Arg), whereas its 3 products are AMP, diphosphate, and L-arginyl-tRNA(Arg).

This enzyme belongs to the family of ligases, to be specific those forming carbon-oxygen bonds in aminoacyl-tRNA and related compounds. The systematic name of this enzyme class is L-arginine:tRNAArg ligase (AMP-forming). Other names in common use include arginyl-tRNA synthetase, arginyl-transfer ribonucleate synthetase, arginyl-transfer RNA synthetase, arginyl transfer ribonucleic acid synthetase, arginine-tRNA synthetase, and arginine translase. This enzyme participates in arginine and proline metabolism and aminoacyl-trna biosynthesis.

It contains a conserved domain at the N terminus called arginyl tRNA synthetase N terminal domain or additional domain 1 (Add-1). This domain is about 140 residues long and it has been suggested that it is involved in tRNA recognition.[1]

Structural studies

As of late 2007, 4 structures have been solved for this class of enzymes, with PDB accession codes 1BS2, 1F7U, 1F7V, and 1IQ0.

References

  1. ^ Cavarelli J, Delagoutte B, Eriani G, Gangloff J, Moras D (September 1998). "L-arginine recognition by yeast arginyl-tRNA synthetase". EMBO J. 17 (18): 5438–48. doi:10.1093/emboj/17.18.5438. PMC 1170869. PMID 9736621.

Further reading

  • ALLENDE CC, ALLENDE JE (1964). "Purification and Substrate Specificity of Arginyl-Ribonucleic Acid Synthetase from Rat Liver". J. Biol. Chem. 239: 1102–6. PMID 14165914.
  • Mehler AH, Mitra SK (1967). "The activation of arginyl transfer ribonucleic acid synthetase by transfer ribonucleic acid". J. Biol. Chem. 242 (23): 5495–9. PMID 12325365.
  • Mitra SK, Mehler AH (1967). "The arginyl transfer ribonucleic acid synthetase of Escherichia coli". J. Biol. Chem. 242 (23): 5491–5494. PMID 12325364.
This article incorporates text from the public domain Pfam and InterPro: IPR005148


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.

Arginyl tRNA synthetase N terminal domain Provide feedback

This domain is found at the amino terminus of Arginyl tRNA synthetase, also called additional domain 1 (Add-1). It is about 140 residues long and it has been suggested that this domain will be involved in tRNA recognition [1].

Literature references

  1. Cavarelli J, Delagoutte B, Eriani G, Gangloff J, Moras D; , EMBO J 1998;17:5438-5448.: L-arginine recognition by yeast arginyl-tRNA synthetase. PUBMED:9736621 EPMC:9736621


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005148

The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction [ PUBMED:10704480 , PUBMED:12458790 ]. 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, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. 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 [ PUBMED:10447505 ].

This domain is found at the N terminus of Arginyl tRNA synthetase, also called additional domain 1 (Add-1). It is about 140 residues long and it has been suggested to be involved in tRNA recognition [ PUBMED:9736621 ].

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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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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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
(105)
Full
(10406)
Representative proteomes UniProt
(49382)
RP15
(1532)
RP35
(5090)
RP55
(10432)
RP75
(17399)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

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  Seed
(105)
Full
(10406)
Representative proteomes UniProt
(49382)
RP15
(1532)
RP35
(5090)
RP55
(10432)
RP75
(17399)
Alignment:
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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
(105)
Full
(10406)
Representative proteomes UniProt
(49382)
RP15
(1532)
RP35
(5090)
RP55
(10432)
RP75
(17399)
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: Bateman A
Previous IDs: N-Arg;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 105
Number in full: 10406
Average length of the domain: 86.80 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 15.04 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.5 21.5
Trusted cut-off 21.5 21.5
Noise cut-off 21.4 21.4
Model length: 85
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

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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 Arg_tRNA_synt_N domain has been found. There are 28 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
A0A0P0UYI0 View 3D Structure Click here
A0A0R0HRN5 View 3D Structure Click here
A0A1D6FU97 View 3D Structure Click here
A0A1D6LYR0 View 3D Structure Click here
A0A2R8QMS9 View 3D Structure Click here
A0B5P0 View 3D Structure Click here
A0L5I2 View 3D Structure Click here
A1A3B6 View 3D Structure Click here
A1AVC2 View 3D Structure Click here
A1B373 View 3D Structure Click here
A1BJV9 View 3D Structure Click here
A1K2E2 View 3D Structure Click here
A1R7X2 View 3D Structure Click here
A1S2P7 View 3D Structure Click here
A1SQW6 View 3D Structure Click here
A1TD77 View 3D Structure Click here
A1TJ83 View 3D Structure Click here
A1UK06 View 3D Structure Click here
A1USU3 View 3D Structure Click here
A1VTL9 View 3D Structure Click here
A1WZR7 View 3D Structure Click here
A2SC26 View 3D Structure Click here
A2STL6 View 3D Structure Click here
A3DGS4 View 3D Structure Click here
A3Q9V2 View 3D Structure Click here
A4FN47 View 3D Structure Click here
A4G1E2 View 3D Structure Click here
A4I2T4 View 3D Structure Click here
A4J9D2 View 3D Structure Click here
A4SGY3 View 3D Structure Click here
A4VH02 View 3D Structure Click here
A4VYA3 View 3D Structure Click here
A4XPN9 View 3D Structure Click here
A4YV78 View 3D Structure Click here
A5CD00 View 3D Structure Click here
A5EXU4 View 3D Structure Click here
A5G3W5 View 3D Structure Click here
A5GP97 View 3D Structure Click here
A5GW85 View 3D Structure Click here
A5I0R5 View 3D Structure Click here