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263  structures 37547  species 21  interactions 129814  sequences 180  architectures

Family: GTP_EFTU_D2 (PF03144)

Summary: Elongation factor Tu domain 2

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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.

Elongation factor Tu domain 2 Provide feedback

Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to PF03143 and in fact has weak sequence matches to this domain.

Literature references

  1. Nissen P, Kjeldgaard M, Thirup S, Polekhina G, Reshetnikova L, Clark BF, Nyborg J; , Science 1995;270:1464-1472.: Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog. PUBMED:7491491 EPMC:7491491


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004161

Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [PUBMED:12762045, PUBMED:15922593, PUBMED:12932732]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution.

EF1A (also known as EF-1alpha or EF-Tu) is a G-protein. It forms a ternary complex of EF1A-GTP-aminoacyltRNA. The binding of aminoacyl-tRNA stimulates GTP hydrolysis by EF1A, causing a conformational change in EF1A that causes EF1A-GDP to detach from the ribosome, leaving the aminoacyl-tRNA attached at the A-site. Only the cognate aminoacyl-tRNA can induce the required conformational change in EF1A through its tight anticodon-codon binding [PUBMED:15680978, PUBMED:12102560]. EF1A-GDP is returned to its active state, EF1A-GTP, through the action of another elongation factor, EF1B (also known as EF-Ts or EF-1beta/gamma/delta).

EF1A consists of three structural domains. This entry represents domain 2 of EF2, which adopts a beta-barrel structure, and is involved in binding to both charged tRNA [PUBMED:7491491]. This domain is structurally related to the C-terminal domain of EF2 (INTERPRO), to which it displays weak sequence matches. This domain is also found in other proteins such as translation initiation factor IF-2 and tetracycline-resistance proteins.

More information about these proteins can be found at Protein of the Month: Elongation Factors [PUBMED:].

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 EFTPs (CL0575), which has the following description:

This superfamily is characterised ba a barrel that is formed as a greek-key. It is found as the second domain in many elongation factor proteins, as well as in an elaborated from in two ribosomal proteins and in some other N-terminal domains, eg of AlaX and Gar1 and RimM protein famlies.

The clan contains the following 7 members:

Gar1 GTP_EFTU_D2 NSP2_assoc RIBIOP_C Ribosomal_L3 Ribosomal_L35Ae RimM

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...

View options

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
(196)
Full
(129814)
Representative proteomes NCBI
(65514)
Meta
(7388)
RP15
(2908)
RP35
(6815)
RP55
(9973)
RP75
(12842)
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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
(196)
Full
(129814)
Representative proteomes NCBI
(65514)
Meta
(7388)
RP15
(2908)
RP35
(6815)
RP55
(9973)
RP75
(12842)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(196)
Full
(129814)
Representative proteomes NCBI
(65514)
Meta
(7388)
RP15
(2908)
RP35
(6815)
RP55
(9973)
RP75
(12842)
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: Prosite
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 196
Number in full: 129814
Average length of the domain: 69.70 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 13.39 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 30.0 30.0
Trusted cut-off 30.0 30.0
Noise cut-off 29.9 29.9
Model length: 74
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Interactions

There are 21 interactions for this family. More...

Ribosom_S12_S23 EFG_IV RNA_replicase_B GTP_EFTU_D3 GTP_EFTU_D2 eRF1_2 GTP_EFTU_D3 eIF2_C EFG_II GTP_EFTU Ribosom_S12_S23 eIF2_C IF-2 GTP_EFTU EF1_GNE eIF-5_eIF-2B eRF1_1 PAPS_reduct EIF_2_alpha eRF1_1 Ribosomal_S25

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 GTP_EFTU_D2 domain has been found. There are 263 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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