This is the Wikipedia entry entitled "EIF-W2 protein domain". More...
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EIF-W2 protein domain Edit Wikipedia article
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crystal structure of the catalytic fragment of eukaryotic initiation factor 2b epsilon
In molecular biology, the protein domaineIF4-gamma/eIF5/eIF2-epsilon is a family of evolutionarily related proteins. This domain is found at the C-terminus of several translation Initiation factors. It was first detected at the very C-termini of the yeast protein GCD6, eIF-2B epsilon, and two other eukaryotic translation initiation factors, eIF-4 gamma and eIF-5 and it may be involved in the interaction of eIF-2B, eIF-4 gamma, and eIF-5 with eIF-2.
In molecular biology, the eIF-W2 domain functions as the binding site for Mnk eIF4E kinase, an enzyme that phosphorylates eukaryotic initiation factor 4E (eIF4E). For eIF2B-epsilon, the W2 C-terminal domain functions in guanine nucleotide exchange on eIF2. For eIF5, the W2 domain functions in mediating the multifactor complex (MFC) formation with eIF1, eIF2-GTP, eIF3 and Met-tRNAiMet. The eIF5 W2 C-terminal domain and the adjacent N-terminal linker region is responsible for the GDI activity against eIF2-GDP.
The W2 domain has a globular fold and is exclusively composed out of alpha-helices. The structure can be divided into a structural C-terminal core onto which the two N-terminal helices are attached. The core contains two aromatic/acidic residue-rich regions (AA boxes), which are important for mediating protein-protein interactions.
This entry covers the entire W2 domain, which is part of the TPR clan.
Translation initiation is a well regulated and highly coordinated cellular process in eukaryotes, in which at least 11 eukaryotic initiation factors (eIFs) are included. These factors come together to form the pre-initiation complex.
Eukaryotic initiation factors
- Eukaryotic translation initiation factor 4 gamma (eIF-4-gamma) 
- Eukaryotic translation initiation factor 5 (eIF-5), a GTPase-activating protein (GAP) specific for eIF2 
- Koonin EV (1995). "Multidomain organization of eukaryotic guanine nucleotide exchange translation initiation factor eIF-2B subunits revealed by analysis of conserved sequence motifs". Protein Sci. 4 (8): 1608â€“1617. doi:10.1002/pro.5560040819. PMC 2143190. PMID 8520487.
- Singh CR, Watanabe R, Zhou D, Jennings MD, Fukao A, Lee B et al. (2011). "Mechanisms of translational regulation by a human eIF5-mimic protein.". Nucleic Acids Res 39 (19): 8314â€“28. doi:10.1093/nar/gkr339. PMC 3201852. PMID 21745818.
- Fukunaga R, Hunter T (1997). "MNK1, a new MAP kinase-activated protein kinase, isolated by a novel expression screening method for identifying protein kinase substrates.". EMBO J 16 (8): 1921â€“33. doi:10.1093/emboj/16.8.1921. PMC 1169795. PMID 9155018.
- Boesen T, Mohammad SS, Pavitt GD, Andersen GR (March 2004). "Structure of the catalytic fragment of translation initiation factor 2B and identification of a critically important catalytic residue". J. Biol. Chem. 279 (11): 10584â€“92. doi:10.1074/jbc.M311055200. PMID 14681227.
- Wei Z, Xue Y, Xu H, Gong W (May 2006). "Crystal structure of the C-terminal domain of S.cerevisiae eIF5". J. Mol. Biol. 359 (1): 1â€“9. doi:10.1016/j.jmb.2006.03.037. PMID 16616930.
- Bieniossek C, SchÃƒÂ¼tz P, Bumann M, Limacher A, Uson I, Baumann U (July 2006). "The crystal structure of the carboxy-terminal domain of human translation initiation factor eIF5". J. Mol. Biol. 360 (2): 457â€“65. doi:10.1016/j.jmb.2006.05.021. PMID 16781736.
- Koonin EV (August 1995). "Multidomain organization of eukaryotic guanine nucleotide exchange translation initiation factor eIF-2B subunits revealed by analysis of conserved sequence motifs". Protein Sci. 4 (8): 1608â€“17. doi:10.1002/pro.5560040819. PMC 2143190. PMID 8520487.
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.
eIF4-gamma/eIF5/eIF2-epsilon Provide feedback
This domain of unknown function is found at the C-terminus of several translation initiation factors .
Koonin EV; , Protein Sci 1995;4:1608-1617.: Multidomain organization of eukaryotic guanine nucleotide exchange translation initiation factor eIF-2B subunits revealed by analysis of conserved sequence motifs. PUBMED:8520487 EPMC:8520487
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR003307
Translation initiation is a sophisticated, well regulated and highly coordinated cellular process in eukaryotes, in which at least 11 eukayrotic initiation factors (eIFs) are included. The W2 domain (two invariant tryptophans) is a region of ~165 amino acids which is found in the C terminus of the following eIFs [PUBMED:8520487, PUBMED:10958635, PUBMED:14681227, PUBMED:16616930, PUBMED:16781736]:
- Eukaryotic translation initiation factor 2B epsilon (eIF-2B-epsilon).
- Eukaryotic translation initiation factor 4 gamma (eIF-4-gamma).
- Eukaryotic translation initiation factor 5 (eIF-5), a GTPase-activating protein (GAP) specific for eIF2.
The W2 domain has a globular fold and is exclusively composed out of alpha- helices [PUBMED:14681227, PUBMED:16616930, PUBMED:16781736]. The structure can be divided into a structural C-terminal core onto which the two N-terminal helices are attached. The core contains two aromatic/acidic residue-rich regions (AA boxes), which are important for mediating protein-protein interactions.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||protein binding (GO:0005515)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
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Tetratricopeptide-like repeats are found in a numerous and diverse proteins involved in such functions as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding.
The clan contains the following 127 members:Adaptin_N Alkyl_sulf_dimr ANAPC3 ANAPC5 API5 Arm Arm_2 Arm_3 Avirulence BTAD CAS_CSE1 ChAPs CLASP_N Clathrin Clathrin-link Clathrin_propel Cnd1 Cnd3 Coatomer_E Cohesin_HEAT Cohesin_load COPI_C CRM1_C Cse1 DNA_alkylation Drf_FH3 Drf_GBD DUF1822 DUF2225 DUF3385 DUF3458 DUF3808 DUF3856 DUF4042 DUF924 EST1 EST1_DNA_bind FAT Fis1_TPR_C Fis1_TPR_N Foie-gras_1 GUN4_N HAT HEAT HEAT_2 HEAT_EZ HEAT_PBS HemY_N IBB IBN_N IFRD KAP Leuk-A4-hydro_C LRV LRV_FeS MA3 MIF4G MIF4G_like MIF4G_like_2 Mo25 MRP-S27 NARP1 Neurochondrin Nipped-B_C Nro1 NSF Paf67 ParcG PC_rep PHAT PI3Ka PknG_TPR PPP5 PPR PPR_1 PPR_2 PPR_3 PPTA Proteasom_PSMB PUF Rab5-bind Rapsyn_N RPN7 Sel1 SHNi-TPR SNAP SPO22 SRP_TPR_like ST7 Suf SusD SusD-like SusD-like_2 SusD-like_3 TAF6_C TAtT Tcf25 TOM20_plant TPR_1 TPR_10 TPR_11 TPR_12 TPR_14 TPR_15 TPR_16 TPR_17 TPR_18 TPR_19 TPR_2 TPR_20 TPR_21 TPR_3 TPR_4 TPR_5 TPR_6 TPR_7 TPR_8 TPR_9 Upf2 V-ATPase_H_C V-ATPase_H_N Vac14_Fab1_bd Vitellogenin_N Vps39_1 W2 Xpo1 YfiO
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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Curation and family details
|Number in seed:||413|
|Number in full:||2073|
|Average length of the domain:||81.20 aa|
|Average identity of full alignment:||29 %|
|Average coverage of the sequence by the domain:||12.41 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||14|
|Download:||download the raw HMM for this family|
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 W2 domain has been found. There are 14 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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