Summary: Elongation factor P (EF-P) OB domain
Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.
This is the Wikipedia entry entitled "Elongation factor P". More...
Elongation factor P Edit Wikipedia article
Elongation factor P (EF-P) KOW-like domain | |||||||||
---|---|---|---|---|---|---|---|---|---|
![]() crystal structure of translation initiation factor 5a from pyrococcus horikoshii | |||||||||
Identifiers | |||||||||
Symbol | EFP_N | ||||||||
Pfam | PF08207 | ||||||||
Pfam clan | CL0107 | ||||||||
InterPro | IPR013185 | ||||||||
PROSITE | PDOC00981 | ||||||||
|
Elongation factor P (EF-P) OB domain | |||||||||
---|---|---|---|---|---|---|---|---|---|
![]() crystal structure of translation elongation factor p from thermus thermophilus hb8 | |||||||||
Identifiers | |||||||||
Symbol | EFP | ||||||||
Pfam | PF01132 | ||||||||
Pfam clan | CL0021 | ||||||||
InterPro | IPR001059 | ||||||||
PROSITE | PDOC00981 | ||||||||
CDD | cd04470 | ||||||||
|
Elongation factor P, C-terminal | |||||||||
---|---|---|---|---|---|---|---|---|---|
![]() crystal structure of translation elongation factor p from thermus thermophilus hb8 | |||||||||
Identifiers | |||||||||
Symbol | Elong-fact-P_C | ||||||||
Pfam | PF09285 | ||||||||
InterPro | IPR015365 | ||||||||
SCOPe | 1ueb / SUPFAM | ||||||||
CDD | cd05794 | ||||||||
|
EF-P (elongation factor P) is a prokaryotic protein translation factor required for efficient peptide bond synthesis on 70S ribosomes from fMet-tRNAfMet.[1] It probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase.
EF-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[2]
- A C-terminal domain which adopts an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology[2]
eIF5A is the eukaryotic homolog of EF-P.
Function
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.[3] Additionally, EF-P has been shown to assist in efficient translation of three or more consecutive proline residues.[4]
See also
- Prokaryotic elongation factors
- EF-Ts (elongation factor thermo stable)
- EF-Tu (elongation factor thermo unstable)
- EF-G (elongation factor G)
- EIF5A
- Protein translation
- GTPase
References
- ^ 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.
- ^ a b 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. Bibcode:2004PNAS..101.9595H. doi:10.1073/pnas.0308667101. PMC 470720. PMID 15210970.
- ^ Leaps in Translational Elongation Science (2009) 326, 677.
- ^ Ude, Susanne; Lassak, Jürgen; Starosta, Agata L.; Kraxenberger, Tobias; Wilson, Daniel N.; Jung, Kirsten (2013-01-04). "Translation Elongation Factor EF-P Alleviates Ribosome Stalling at Polyproline Stretches". Science. 339 (6115): 82–85. Bibcode:2013Sci...339...82U. doi:10.1126/science.1228985. ISSN 0036-8075. PMID 23239623.
This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.
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 P (EF-P) OB domain Provide feedback
No Pfam abstract.
External database links
PROSITE: | PDOC00981 |
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, PUBMED:9405429]. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively.
EF-P has 3 domains (domains I, II, and III). Domains II and III are S1-like domains and have structural homology to the eIF5A domain C, suggesting that domains II and III evolved by duplication. 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].
Gene Ontology
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) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
Loading domain graphics...
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 110 members:
BOF BRCA-2_OB1 BRCA-2_OB3 CcmE CDC13_N Cdc13_OB2 CDC24_OB1 CDC24_OB2 CDC24_OB3 CSD CSD2 CusF_Ec CysA_C_terminal DNA_ligase_A_C DNA_ligase_C DNA_ligase_OB DNA_ligase_OB_2 DNA_pol_D_N DUF1344 DUF1449 DUF2110 DUF223 DUF2815 DUF3127 DUF3217 DUF3299 DUF4539 DUF5666 DUF961 EFP eIF-1a eIF-5a Elong-fact-P_C EutN_CcmL EXOSC1 FbpC_C_terminal Fimbrial_PilY2 GlcV_C_terminal Gp138_N gp32 Gp5_OB HIN ID MCM_OB mRNA_cap_C MRP-S35 NfeD NigD_N NlpE_C OB_aCoA_assoc OB_Dis3 OB_MalK OB_NTP_bind OB_RNB PCB_OB Phage_base_V Phage_DNA_bind Phage_SSB Pol_alpha_B_N POT1 POT1PC Prot_ATP_ID_OB Prot_ATP_OB_N RecG_wedge RecJ_OB RecO_N RecO_N_2 Rep-A_N Rep_fac-A_3 Rep_fac-A_C REPA_OB_2 Rho_RNA_bind Ribosom_S12_S23 Ribosomal_L2 Ribosomal_S17 Ribosomal_S28e Ribosomal_S4e RMI1_C RMI1_N RMI2 RNA_pol_Rbc25 RNA_pol_Rpb8 RNA_pol_RpbG RNase_II_C_S1 RPA43_OB Rrp44_CSD1 Rrp44_S1 RsgA_N RuvA_N S1 S1-like S1_2 SfsA_N SSB ssDBP Stn1 TEBP_beta Ten1 Ten1_2 TOBE TOBE_2 TOBE_3 TPP1 TRAM TRAM_2 tRNA_anti-codon tRNA_anti-like tRNA_anti_2 tRNA_bind TTC5_OBAlignments
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, the UniProtKB sequence database, 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 (730) |
Full (7718) |
Representative proteomes | UniProt (35721) |
NCBI (30068) |
Meta (2186) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (1015) |
RP35 (3746) |
RP55 (7706) |
RP75 (13440) |
||||||
Jalview | |||||||||
HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
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 (730) |
Full (7718) |
Representative proteomes | UniProt (35721) |
NCBI (30068) |
Meta (2186) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (1015) |
RP35 (3746) |
RP55 (7706) |
RP75 (13440) |
||||||
Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | Prosite |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
Number in seed: | 730 |
Number in full: | 7718 |
Average length of the domain: | 53.70 aa |
Average identity of full alignment: | 33 % |
Average coverage of the sequence by the domain: | 28.32 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
|
||||||||||||
Model details: |
|
||||||||||||
Model length: | 54 | ||||||||||||
Family (HMM) version: | 21 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
Sunburst controls
HideWeight segments by...
Change the size of the sunburst
Colour assignments
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
Selections
Align selected sequences to HMM
Generate a FASTA-format file
Clear selection
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...
Tree controls
HideThe tree shows the occurrence of this domain across different species. More...
Loading...
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
Interactions
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 EFP domain has been found. There are 18 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.
Loading structure mapping...