Summary: Elongation factor P, C-terminal
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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
|SCOPe||1ueb / SUPFAM|
EF-P (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.
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
- 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. Additionally, EF-P has been shown to assist in efficient translation of three or more consecutive proline residues.
- Prokaryotic elongation factors
- EF-Ts (elongation factor thermo stable)
- EF-Tu (elongation factor thermo unstable)
- EF-G (elongation factor G)
- Protein translation
- 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): 7â€“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): 9595â€“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, JÃ¼rgen; 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): 82â€“85. Bibcode:2013Sci...339...82U. doi:10.1126/science.1228985. ISSN 0036-8075. PMID 23239623.
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Elongation factor P, C-terminal Provide feedback
Members of this family of nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology .
Hanawa-Suetsugu K, Sekine S, Sakai H, Hori-Takemoto C, Terada T, Unzai S, Tame JR, Kuramitsu S, Shirouzu M, Yokoyama S; , Proc Natl Acad Sci U S A. 2004;101:9595-9600.: Crystal structure of elongation factor P from Thermus thermophilus HB8. PUBMED:15210970 EPMC:15210970
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR015365
Elongation factor P (EF-P) stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. 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 [ PUBMED:9405429 , PUBMED:16928980 , PUBMED:15922593 , PUBMED:12932732 ]. 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. This entry includes domain III (the second S1 domain of EF_P). Domains II and III of have structural homology to the eIF5A domain C, suggesting that domains II and III evolved by duplication. These domains adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology [ PUBMED:15210970 ].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||cytoplasm (GO:0005737)|
|Biological process||peptide biosynthetic process (GO:0043043)|
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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 113 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 DUF5666 DUF6484 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 HROB 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 TLP1_add_C TOBE TOBE_2 TOBE_3 TPP1 TRAM TRAM_2 tRNA_anti-codon tRNA_anti-like tRNA_anti_2 tRNA_bind TTC5_OB WCOB
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Key: available, not generated, — not available.
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|Number in seed:||372|
|Number in full:||9379|
|Average length of the domain:||56.00 aa|
|Average identity of full alignment:||48 %|
|Average coverage of the sequence by the domain:||29.42 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||14|
|Download:||download the raw HMM for this family|
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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 Elong-fact-P_C domain has been found. There are 20 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.