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236  structures 4195  species 0  interactions 11102  sequences 118  architectures

Family: IF-2B (PF01008)

Summary: Initiation factor 2 subunit family

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Initiation factor 2 subunit family Provide feedback

This family includes initiation factor 2B alpha, beta and delta subunits from eukaryotes, initiation factor 2B subunits 1 and 2 from archaebacteria and some proteins of unknown function from prokaryotes. Initiation factor 2 binds to Met-tRNA, GTP and the small ribosomal subunit. Members of this family have also been characterised as 5-methylthioribose- 1-phosphate isomerases, an enzyme of the methionine salvage pathway. The crystal structure of Ypr118w, a non-essential, low-copy number gene product from Saccharomyces cerevisiae, reveals a dimeric protein with two domains and a putative active site cleft [2].

Literature references

  1. Kyrpides NC, Woese CR; , Proc Natl Acad Sci U S A 1998;95:3726-3730.: Archaeal translation initiation revisited: the initiation factor 2 and eukaryotic initiation factor 2B alpha-beta-delta subunit families. PUBMED:9520434 EPMC:9520434

  2. Bumann M, Djafarzadeh S, Oberholzer AE, Bigler P, Altmann M, Trachsel H, Baumann U; , J Biol Chem 2004; [Epub ahead of print]: Crystal structure of yeast Ypr118w, a methylthioribose-1-phosphate isomerase related to regulatory eIF2B subunits. PUBMED:15215245 EPMC:15215245


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000649

Initiation factor 2 binds to Met-tRNA, GTP and the small ribosomal subunit. The eukaryotic translation initiation factor EIF-2B is a complex made up of five different subunits, alpha, beta, gamma, delta and epsilon, and catalyses the exchange of EIF-2-bound GDP for GTP. This family includes initiation factor 2B alpha, beta and delta subunits from eukaryotes; related proteins from archaebacteria and IF-2 from prokaryotes and also contains a subfamily of proteins in eukaryotes, archaeae (e.g. Pyrococcus furiosus), or eubacteria such as Bacillus subtilis and Thermotoga maritima. Many of these proteins were initially annotated as putative translation initiation factors despite the fact that there is no evidence for the requirement of an IF2 recycling factor in prokaryotic translation initiation. Recently, one of these proteins from B. subtilis has been functionally characterised as a 5-methylthioribose-1-phosphate isomerase (MTNA) [ PUBMED:14551435 ]. This enzyme participates in the methionine salvage pathway catalysing the isomerisation of 5-methylthioribose-1-phosphate to 5-methylthioribulose-1-phosphate [ PUBMED:15215245 ]. The methionine salvage pathway leads to the synthesis of methionine from methylthioadenosine, the end product of the spermidine and spermine anabolism in many species.

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 ISOCOT_Fold (CL0246), which has the following description:

This superfamily contains a variety of enzymes and non-enzymatic ligand binding domains.

The clan contains the following 12 members:

5-FTHF_cyc-lig AcetylCoA_hyd_C AcetylCoA_hydro CitF CoA_trans DeoRC Glucosamine_iso IF-2B LUD_dom Mal_decarbox_Al Rib_5-P_isom_A Sugar-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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(18)
Full
(11102)
Representative proteomes UniProt
(33813)
RP15
(2060)
RP35
(5398)
RP55
(9440)
RP75
(14074)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(18)
Full
(11102)
Representative proteomes UniProt
(33813)
RP15
(2060)
RP35
(5398)
RP55
(9440)
RP75
(14074)
Alignment:
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Sequence:
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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
(18)
Full
(11102)
Representative proteomes UniProt
(33813)
RP15
(2060)
RP35
(5398)
RP55
(9440)
RP75
(14074)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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_1302 (release 3.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 18
Number in full: 11102
Average length of the domain: 278.80 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 72.63 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.4 22.4
Trusted cut-off 22.4 22.4
Noise cut-off 22.3 22.3
Model length: 282
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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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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 IF-2B domain has been found. There are 236 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A096SRR1 View 3D Structure Click here
A0A0P0XUJ0 View 3D Structure Click here
A0A0R0F3P0 View 3D Structure Click here
A0A0R0G2K6 View 3D Structure Click here
A0A0R0IB61 View 3D Structure Click here
A0A0R4ILD9 View 3D Structure Click here
A0A0R4ITG6 View 3D Structure Click here
A0A1D6GLI2 View 3D Structure Click here
A0A1D6GR68 View 3D Structure Click here
A0A1D6KGC9 View 3D Structure Click here
A0A1D8PH13 View 3D Structure Click here
A0A1D8PQT4 View 3D Structure Click here
A0A1P8AT59 View 3D Structure Click here
A0A1P8AVS2 View 3D Structure Click here
A0A286Y8J6 View 3D Structure Click here
A4HUK8 View 3D Structure Click here
A4HV45 View 3D Structure Click here
A4I2S1 View 3D Structure Click here
A4ICE5 View 3D Structure Click here
A9JRE2 View 3D Structure Click here
B3H7H1 View 3D Structure Click here
B4FA42 View 3D Structure Click here
B6TJL9 View 3D Structure Click here
B6TZD1 View 3D Structure Click here
F4HTE0 View 3D Structure Click here
F4I048 View 3D Structure Click here
F4IT40 View 3D Structure Click here
G5EFF9 View 3D Structure Click here
I1JS74 View 3D Structure Click here
I1KD70 View 3D Structure Click here
I1KHI7 View 3D Structure Click here
I1KIW2 View 3D Structure Click here
I1LLC8 View 3D Structure Click here
I1LX09 View 3D Structure Click here
I1M2R6 View 3D Structure Click here
I1MUH1 View 3D Structure Click here
I1N6M9 View 3D Structure Click here
K7MV73 View 3D Structure Click here
O60185 View 3D Structure Click here
O76863 View 3D Structure Click here
P12754 View 3D Structure Click here
P14741 View 3D Structure Click here
P32502 View 3D Structure Click here
P34604 View 3D Structure Click here
P49770 View 3D Structure Click here
Q06489 View 3D Structure Click here
Q09924 View 3D Structure Click here
Q0DQ10 View 3D Structure Click here
Q0ITU1 View 3D Structure Click here
Q14232 View 3D Structure Click here
Q2QM52 View 3D Structure Click here
Q2QQD9 View 3D Structure Click here
Q4CS37 View 3D Structure Click here
Q4CY36 View 3D Structure Click here
Q4D5Q3 View 3D Structure Click here
Q4D6B2 View 3D Structure Click here
Q4DKT2 View 3D Structure Click here
Q4DW27 View 3D Structure Click here
Q4E0M1 View 3D Structure Click here
Q54EY2 View 3D Structure Click here
Q54FM3 View 3D Structure Click here
Q54I81 View 3D Structure Click here
Q54R90 View 3D Structure Click here
Q57586 View 3D Structure Click here
Q57896 View 3D Structure Click here
Q5AD59 View 3D Structure Click here
Q5ADR6 View 3D Structure Click here
Q5ADR6 View 3D Structure Click here
Q5HZE4 View 3D Structure Click here
Q61749 View 3D Structure Click here
Q62818 View 3D Structure Click here
Q63186 View 3D Structure Click here
Q64270 View 3D Structure Click here
Q8I4S8 View 3D Structure Click here
Q8IBB6 View 3D Structure Click here
Q8IJQ6 View 3D Structure Click here
Q93169 View 3D Structure Click here
Q99LC8 View 3D Structure Click here
Q99LD9 View 3D Structure Click here
Q9BV20 View 3D Structure Click here
Q9CQT1 View 3D Structure Click here
Q9FFV8 View 3D Structure Click here
Q9UI10 View 3D Structure Click here
Q9USP0 View 3D Structure Click here
Q9UT76 View 3D Structure Click here
Q9V9X4 View 3D Structure Click here
Q9VAD4 View 3D Structure Click here
Q9W1Q8 View 3D Structure Click here
Q9XWD5 View 3D Structure Click here
Q9ZUG4 View 3D Structure Click here