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27  structures 4697  species 3  interactions 5864  sequences 45  architectures

Family: B3_4 (PF03483)

Summary: B3/4 domain

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This is the Wikipedia entry entitled "B3 4". More...

B3 4 Edit Wikipedia article

B3_4
PDB 2iy5 EBI.jpg
phenylalanyl-trna synthetase from thermus thermophilus complexed with trna and a phenylalanyl-adenylate analog
Identifiers
Symbol B3_4
Pfam PF03483
Pfam clan CL0383
InterPro IPR005146
SCOP 1pys
SUPERFAMILY 1pys

This entry represents the B3/B4 domain, which in molecular biology is found in tRNA synthetase beta subunits, as well as in some non-tRNA synthetase proteins.

Function[edit]

In molecular biology, aminoacyl-tRNA synthetases can catalyse editing reactions to correct errors produced during amino acid activation and tRNA esterification, in order to prevent the attachment of incorrect amino acids to tRNA. The B3/B4 domain of the beta subunit contains an editing site, which lies close to the active site on the alpha subunit.[1] Disruption of this site abolished tRNA editing, a process that is essential for faithful translation of the genetic code.

Structure[edit]

This domain has a 3-layer structure, and contains a beta-sandwich fold of unusual topology, and contains a putative tRNA-binding structural motif.[2] In Thermus thermophilus, both the catalytic alpha- and the non-catalytic beta-subunits comprise the characteristic fold of the class II active-site domains. The presence of an RNA-binding domain, similar to that of the U1A spliceosomal protein, in the beta-subunit of tRNA synthetase indicates structural relationships among different families of RNA-binding proteins.

References[edit]

  1. ^ Roy H, Ling J, Irnov M, Ibba M (November 2004). "Post-transfer editing in vitro and in vivo by the beta subunit of phenylalanyl-tRNA synthetase". EMBO J. 23 (23): 4639–48. doi:10.1038/sj.emboj.7600474. PMC 533057. PMID 15526031. 
  2. ^ Mosyak L, Reshetnikova L, Goldgur Y, Delarue M, Safro MG (July 1995). "Structure of phenylalanyl-tRNA synthetase from Thermus thermophilus". Nat. Struct. Biol. 2 (7): 537–47. doi:10.1038/nsb0795-537. PMID 7664121. 

This article incorporates text from the public domain Pfam and InterPro IPR005146

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.

B3/4 domain Provide feedback

This domain is found in tRNA synthetase beta subunits as well as in some non tRNA synthetase proteins.

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 IPR005146

This entry represents the B3/B4 domain found in tRNA synthetase beta subunits as well as in some non-tRNA synthetase proteins. This domain has a 3-layer structure, and contains a beta-sandwich fold of unusual topology, and contains a putative tRNA-binding structural motif [PUBMED:7664121]. In Thermus thermophilus, both the catalytic alpha- and the non-catalytic beta-subunits comprise the characteristic fold of the class II active-site domains. The presence of an RNA-binding domain, similar to that of the U1A spliceosomal protein, in the beta-subunit of tRNA synthetase indicates structural relationships among different families of RNA-binding proteins.

Aminoacyl-tRNA synthetases can catalyse editing reactions to correct errors produced during amino acid activation and tRNA esterification, in order to prevent the attachment of incorrect amino acids to tRNA. The B3/B4 domain of the beta subunit contains an editing site, which lies close to the active site on the alpha subunit [PUBMED:15526031]. Disruption of this site abolished tRNA editing, a process that is essential for faithful translation of the genetic code.

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 PheT-TilS (CL0383), which has the following description:

Families here are thought to contain a putative tRNA-binding structural motif. The families are the C-terminal domains of tRNA-Ile-lysidine and the phenylalanine-tRNA synthetases.

The clan contains the following 2 members:

B3_4 TilS_C

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
(308)
Full
(5864)
Representative proteomes NCBI
(4739)
Meta
(2917)
RP15
(509)
RP35
(955)
RP55
(1269)
RP75
(1517)
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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
(308)
Full
(5864)
Representative proteomes NCBI
(4739)
Meta
(2917)
RP15
(509)
RP35
(955)
RP55
(1269)
RP75
(1517)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(308)
Full
(5864)
Representative proteomes NCBI
(4739)
Meta
(2917)
RP15
(509)
RP35
(955)
RP55
(1269)
RP75
(1517)
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_1005 (release 7.0)
Previous IDs: S3_4;
Type: Domain
Author: Bateman A
Number in seed: 308
Number in full: 5864
Average length of the domain: 167.50 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 24.80 %

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 23.3 23.3
Trusted cut-off 23.4 23.3
Noise cut-off 23.2 23.2
Model length: 174
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 3 interactions for this family. More...

tRNA-synt_2d tRNA_bind B5

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 B3_4 domain has been found. There are 27 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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