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18  structures 1155  species 2  interactions 1277  sequences 39  architectures

Family: ProRS-C_1 (PF09180)

Summary: Prolyl-tRNA synthetase, C-terminal

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Prolyl-tRNA synthetase, C-terminal Provide feedback

Members of this family are predominantly found in prokaryotic prolyl-tRNA synthetase. They contain a zinc binding site, and adopt a structure consisting of alpha helices and antiparallel beta sheets arranged in 2 layers, in a beta-alpha-beta-alpha-beta motif [1].

Literature references

  1. Kamtekar S, Kennedy WD, Wang J, Stathopoulos C, Soll D, Steitz TA; , Proc Natl Acad Sci U S A. 2003;100:1673-1678.: The structural basis of cysteine aminoacylation of tRNAPro by prolyl-tRNA synthetases. PUBMED:12578991 EPMC:12578991


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR016061

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.

Prolyl tRNA synthetase (EC) exists in two forms, which are loosely related. The first form is present in the majority of eubacteria species. The second one, present in some eubacteria, is essentially present in archaea and eukaryota. Prolyl-tRNA synthetase belongs to class IIa.

This domain is found at the C-terminal in archaeal and eukaryotic enzymes, as well as in certain bacterial ones.

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 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
(82)
Full
(1277)
Representative proteomes NCBI
(1221)
Meta
(419)
RP15
(222)
RP35
(375)
RP55
(492)
RP75
(562)
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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
(82)
Full
(1277)
Representative proteomes NCBI
(1221)
Meta
(419)
RP15
(222)
RP35
(375)
RP55
(492)
RP75
(562)
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
(82)
Full
(1277)
Representative proteomes NCBI
(1221)
Meta
(419)
RP15
(222)
RP35
(375)
RP55
(492)
RP75
(562)
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: pdb_1nj1
Previous IDs: none
Type: Domain
Author: Sammut SJ
Number in seed: 82
Number in full: 1277
Average length of the domain: 73.60 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 12.63 %

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 20.9 20.9
Trusted cut-off 21.1 21.0
Noise cut-off 20.6 20.7
Model length: 68
Family (HMM) version: 6
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 HGTP_anticodon

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 ProRS-C_1 domain has been found. There are 18 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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