Summary: Elongation factor P (EF-P) OB domain
This is the Wikipedia entry entitled "Elongation factor P". More...
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Elongation factor P Edit Wikipedia article
|Elongation factor P (EF-P) KOW-like domain|
crystal structure of translation initiation factor 5a from pyrococcus horikoshii
|Elongation factor P (EF-P) OB domain|
crystal structure of translation elongation factor p from thermus thermophilus hb8
|Elongation factor P, C-terminal|
crystal structure of translation elongation factor p from thermus thermophilus hb8
In molecular biology, elongation factor P is a prokaryotic protein translation factor required for efficient peptide bond synthesis on 70S ribosomes from fMet-tRNAfMet. It probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase.
Elongation factor P consists of three domains:
- An N-terminal KOW-like domain
- A central OB domain, which forms an oligonucleotide-binding fold. It is not clear if this region is involved in binding nucleic acids
- A C-terminal domain which adopts an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology
eIF5A is the eukaryotic homolog of EF-P.
It has been suggested that after binding of the initiator tRNA to the P/I site, it is correctly positioned to the P site by binding of EF-P to the E site.
- Aoki H, Adams SL, Turner MA, Ganoza MC (1997). "Molecular characterization of the prokaryotic efp gene product involved in a peptidyltransferase reaction". Biochimie 79 (1): 7–11. doi:10.1016/S0300-9084(97)87619-5. PMID 9195040.
- Hanawa-Suetsugu K, Sekine S, Sakai H, Hori-Takemoto C, Terada T, Unzai S, Tame JR, Kuramitsu S, Shirouzu M, Yokoyama S (June 2004). "Crystal structure of elongation factor P from Thermus thermophilus HB8". Proc. Natl. Acad. Sci. U.S.A. 101 (26): 9595–600. doi:10.1073/pnas.0308667101. PMC 470720. PMID 15210970.
- Leaps in Translational Elongation Science (2009) 326, 677.
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Elongation factor P (EF-P) OB domain Provide feedback
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External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001059
Elongation factor P (EF-P) is a prokaryotic protein translation factor required for efficient peptide bond synthesis on 70S ribosomes from fMet-tRNAfMet [PUBMED:9195040]. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase.
This entry reresents the central domain of elongation factor P and its homologues. It forms an oligonucleotide-binding (OB) fold, though it is not clear if this region is involved in binding nucleic acids [PUBMED:15210970].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||translation elongation factor activity (GO:0003746)|
|Biological process||translational elongation (GO:0006414)|
- the number of sequences which exhibit this architecture
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This example describes an architecture with one
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The OB (oligonucleotide/oligosaccharide binding) was defined by Murzin . 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 .
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
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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Curation and family details
|Author:||Finn RD, Bateman A|
|Number in seed:||271|
|Number in full:||5656|
|Average length of the domain:||55.20 aa|
|Average identity of full alignment:||32 %|
|Average coverage of the sequence by the domain:||29.59 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||15|
|Download:||download the raw HMM for this family|
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There are 2 interactions for this family. More...
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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 EFP domain has been found. There are 12 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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