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51  structures 5178  species 1  interaction 10836  sequences 90  architectures

Family: tRNA-synt_1c (PF00749)

Summary: tRNA synthetases class I (E and Q), catalytic domain

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This is the Wikipedia entry entitled "Aminoacyl tRNA synthetases, class I". More...

Aminoacyl tRNA synthetases, class I Edit Wikipedia article

Glutamyl/glutaminyl-tRNA synthetase, class Ic
Identifiers
Symbol Glu/Gln-tRNA-synth_Ic
Pfam PF00749
InterPro IPR000924

The aminoacyl-tRNA synthetases (EC 6.1.1.) 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.[1] 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.[2] Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices,[3] and are mostly dimeric or multimeric, containing at least three conserved regions.[4][5][6] 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; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases.[7]

Glutamyl-tRNA synthetase (EC 6.1.1.17) is a class Ic synthetase and shows several similarities with glutaminyl-tRNA synthetase concerning structure and catalytic properties. It is an alpha2 dimer. To date one crystal structure of a glutamyl-tRNA synthetase (Thermus thermophilus) has been solved. The molecule has the form of a bent cylinder and consists of four domains. The N-terminal half (domains 1 and 2) contains the 'Rossman fold' typical for class I synthetases and resembles the corresponding part of E. coli GlnRS, whereas the C-terminal half exhibits a GluRS-specific structure.[8]

Human proteins containing this domain

EARS2; EPRS; PIG32; QARS;

References

  1. ^ Delarue M, Moras D, Poch O, Eriani G, Gangloff J (1990). "Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs". Nature 347 (6289): 203–206. doi:10.1038/347203a0. PMID 2203971. 
  2. ^ Moras D, Konno M, Shimada A, Nureki O, Tateno M, Yokoyama S, Sugiura I, Ugaji-Yoshikawa Y, Kuwabara S, Lorber B, Giege R (2000). "The 2.0 A crystal structure of Thermus thermophilus methionyl-tRNA synthetase reveals two RNA-binding modules". Structure 8 (2): 197–208. doi:10.1016/S0969-2126(00)00095-2. PMID 10673435. 
  3. ^ Perona JJ, Steitz TA, Rould MA (1993). "Structural basis for transfer RNA aminoacylation by Escherichia coli glutaminyl-tRNA synthetase". Biochemistry 32 (34): 8758–8771. doi:10.1021/bi00085a006. PMID 8364025. 
  4. ^ Delarue M, Moras D (1993). "The aminoacyl-tRNA synthetase family: modules at work". BioEssays 15 (10): 675–687. doi:10.1002/bies.950151007. PMID 8274143. 
  5. ^ Schimmel P (1991). "Classes of aminoacyl-tRNA synthetases and the establishment of the genetic code". Trends Biochem. Sci. 16 (1): 1–3. doi:10.1016/0968-0004(91)90002-D. PMID 2053131. 
  6. ^ Cusack S, Leberman R, Hartlein M (1991). "Sequence, structural and evolutionary relationships between class 2 aminoacyl-tRNA synthetases". Nucleic Acids Res. 19 (13): 3489–3498. doi:10.1093/nar/19.13.3489. PMC 328370. PMID 1852601. 
  7. ^ Bairoch A (2004). List of aminoacyl-tRNA synthetases. pp. –. 
  8. ^ Soll D, Freist W, Gauss DH, Lapointe J (1997). "Glutamyl-tRNA sythetase". Biol. Chem. 378 (11): 1313–1329. PMID 9426192. 

This article incorporates text from the public domain Pfam and InterPro IPR000924

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.

tRNA synthetases class I (E and Q), catalytic domain Provide feedback

Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only glutamyl and glutaminyl tRNA synthetases. In some organisms, a single glutamyl-tRNA synthetase aminoacylates both tRNA(Glu) and tRNA(Gln).

Literature references

  1. Rath VL, Silvian LF, Beijer B, Sproat BS, Steitz TA; , Structure 1998;6:439-449.: How glutaminyl-tRNA synthetase selects glutamine. PUBMED:9562563 EPMC:9562563


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR020058

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.

Glutamyl-tRNA synthetase (EC) is a class Ic synthetase and shows several similarities with glutaminyl-tRNA synthetase concerning structure and catalytic properties. It is an alpha2 dimer. To date one crystal structure of a glutamyl-tRNA synthetase (Thermus thermophilus) has been solved. The molecule has the form of a bent cylinder and consists of four domains. The N-terminal half (domains 1 and 2) contains the 'Rossman fold' typical for class I synthetases and resembles the corresponding part of Escherichia coli GlnRS, whereas the C-terminal half exhibits a GluRS-specific structure [PUBMED:9426192].

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 HUP (CL0039), which has the following description:

The HUP class contains the HIGH-signature proteins, UspA superfamily and the PP-ATPase superfamily [1]. The HIGH superfamily has the HIGH Nucleotidyl transferases and the class I tRNA synthetases both of which have the HIGH and the KMSKS motif [1],[2]. The PP-loop ATPase named after the ATP PyroPhosphatase domain, was initially identified as a conserved amino acid sequence motif in four distinct groups of enzymes that catalyse the hydrolysis of the alpha-beta phosphate bond of ATP, namely GMP synthetases, argininosuccinate synthetases, asparagine synthetases, and ATP sulfurylases [3]. The USPA superfamily contains USPA, ETFP and Photolyases [1]

The clan contains the following 26 members:

Arginosuc_synth Asn_synthase ATP-sulfurylase ATP_bind_3 ATP_bind_4 Citrate_ly_lig CTP_transf_2 DNA_photolyase ETF FAD_syn HIGH_NTase1 NAD_synthase Pantoate_ligase PAPS_reduct QueC ThiI tRNA-synt_1 tRNA-synt_1_2 tRNA-synt_1b tRNA-synt_1c tRNA-synt_1d tRNA-synt_1e tRNA-synt_1f tRNA-synt_1g tRNA_Me_trans Usp

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
(18)
Full
(10836)
Representative proteomes NCBI
(8426)
Meta
(5158)
RP15
(979)
RP35
(1835)
RP55
(2473)
RP75
(2955)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(18)
Full
(10836)
Representative proteomes NCBI
(8426)
Meta
(5158)
RP15
(979)
RP35
(1835)
RP55
(2473)
RP75
(2955)
Alignment:
Format:
Order:
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
(18)
Full
(10836)
Representative proteomes NCBI
(8426)
Meta
(5158)
RP15
(979)
RP35
(1835)
RP55
(2473)
RP75
(2955)
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: Pfam-B_350 (release 2.1)
Previous IDs: none
Type: Domain
Author: Bateman A, Griffiths-Jones SR
Number in seed: 18
Number in full: 10836
Average length of the domain: 287.60 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 62.06 %

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 19.8 19.8
Trusted cut-off 19.8 19.8
Noise cut-off 19.7 19.2
Model length: 314
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

tRNA-synt_1c_C

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-synt_1c domain has been found. There are 51 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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