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15  structures 539  species 3  interactions 832  sequences 11  architectures

Family: eIF-5a (PF01287)

Summary: Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold

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Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold Provide feedback

eIF5A, previously thought to be an initiation factor, has been shown to be required for peptide chain elongation in yeast [1].

Literature references

  1. Peat TS, Newman J, Waldo GS, Berendzen J, Terwilliger TC; , Structure 1998;6:1207-1214.: Structure of translation initiation factor 5A from Pyrobaculum aerophilum at 1.75 A resolution. PUBMED:9753699 EPMC:9753699

  2. Saini P, Eyler DE, Green R, Dever TE;, Nature. 2009;459:118-121.: Hypusine-containing protein eIF5A promotes translation elongation. PUBMED:19424157 EPMC:19424157


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR020189

A five-stranded beta-barrel was first noted as a common structure among four proteins binding single-stranded nucleic acids (staphylococcal nuclease and aspartyl-tRNA synthetase) or oligosaccharides (B subunits of enterotoxin and verotoxin-1), and has been termed the oligonucleotide/oligosaccharide binding motif, or OB fold, a five-stranded beta-sheet coiled to form a closed beta-barrel capped by an alpha helix located between the third and fourth strands [PUBMED:12769718]. Two ribosomal proteins, S17 and S1, are members of this class, and have different variations of the OB fold theme. Comparisons with other OB fold nucleic acid binding proteins suggest somewhat different mechanisms of nucleic acid recognition in each case [PUBMED:9862955].

There are many nucleic acid-binding proteins that contain domains with this OB-fold structure, including anticodon-binding tRNA synthetases, ssDNA-binding proteins (CDC13, telomere-end binding proteins), phage ssDNA-binding proteins (gp32, gp2.5, gpV), cold shock proteins, DNA ligases, RNA-capping enzymes, DNA replication initiators and RNA polymerase subunit RBP8 [PUBMED:15178340].

This entry represents the RNA-binding domain of translation elongation factor IF5A [PUBMED:19424157].

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 OB (CL0021), which has the following description:

The OB (oligonucleotide/oligosaccharide binding) was defined by Murzin [1]. The common part of the OB-fold, has a five-stranded beta-sheet coiled to form a closed beta-barrel. This barrel is capped by an alpha-helix located between the third and fourth strands [1].

The clan contains the following 45 members:

BOF CSD DNA_ligase_OB DUF2110 DUF223 DUF3127 DUF35 EFP eIF-1a eIF-5a EutN_CcmL EXOSC1 mRNA_cap_C OB_NTP_bind OB_RNB OmdA Phage_DNA_bind POT1 RecO_N RecO_N_2 Rep-A_N Rep_fac-A_3 Rho_RNA_bind Ribosom_S12_S23 Ribosomal_L2 Ribosomal_S17 RNA_pol_Rbc25 RNA_pol_Rpb8 RuvA_N S1 S1-like S1_2 SSB Stn1 TEBP_beta Ten1 Ten1_2 TOBE TOBE_2 TOBE_3 TRAM tRNA_anti-codon tRNA_anti-like tRNA_anti_2 tRNA_bind

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
(97)
Full
(832)
Representative proteomes NCBI
(760)
Meta
(38)
RP15
(143)
RP35
(254)
RP55
(374)
RP75
(474)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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Format an alignment

  Seed
(97)
Full
(832)
Representative proteomes NCBI
(760)
Meta
(38)
RP15
(143)
RP35
(254)
RP55
(374)
RP75
(474)
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
(97)
Full
(832)
Representative proteomes NCBI
(760)
Meta
(38)
RP15
(143)
RP35
(254)
RP55
(374)
RP75
(474)
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: Family
Author: Finn RD, Bateman A, Griffiths-Jones SR
Number in seed: 97
Number in full: 832
Average length of the domain: 66.70 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 40.40 %

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 21.5 21.5
Trusted cut-off 21.6 21.5
Noise cut-off 21.4 21.2
Model length: 69
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Interactions

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

eIF-5a EFP_N KOW

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 eIF-5a domain has been found. There are 15 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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