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10  structures 4549  species 1  interaction 5622  sequences 9  architectures

Family: Elong-fact-P_C (PF09285)

Summary: Elongation factor P, C-terminal

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This is the Wikipedia entry entitled "Elongation factor P". More...

Elongation factor P Edit Wikipedia article

Elongation factor P (EF-P) KOW-like domain
PDB 1iz6 EBI.jpg
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
PDB 1ueb EBI.jpg
crystal structure of translation elongation factor p from thermus thermophilus hb8
Identifiers
Symbol EFP
Pfam PF01132
Pfam clan CL0021
InterPro IPR001059
PROSITE PDOC00981
Elongation factor P, C-terminal
PDB 1ueb EBI.jpg
crystal structure of translation elongation factor p from thermus thermophilus hb8
Identifiers
Symbol Elong-fact-P_C
Pfam PF09285
InterPro IPR015365
SCOP 1ueb
SUPERFAMILY 1ueb

In molecular biology, 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.

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[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[edit]

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]

References[edit]

  1. ^ 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. 
  2. ^ 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. doi:10.1073/pnas.0308667101. PMC 470720. PMID 15210970. 
  3. ^ Leaps in Translational Elongation Science (2009) 326, 677.

This article incorporates text from the public domain Pfam and InterPro IPR001059

This article incorporates text from the public domain Pfam and InterPro IPR015365

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, 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 [1].

Literature references

  1. 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

These 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 [PUBMED:15210970].

Gene Ontology

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Domain organisation

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Alignments

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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
(108)
Full
(5622)
Representative proteomes NCBI
(2891)
Meta
(2007)
RP15
(377)
RP35
(737)
RP55
(951)
RP75
(1133)
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Format an alignment

  Seed
(108)
Full
(5622)
Representative proteomes NCBI
(2891)
Meta
(2007)
RP15
(377)
RP35
(737)
RP55
(951)
RP75
(1133)
Alignment:
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Sequence:
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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
(108)
Full
(5622)
Representative proteomes NCBI
(2891)
Meta
(2007)
RP15
(377)
RP35
(737)
RP55
(951)
RP75
(1133)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

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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.

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Curation and family details

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Seed source: pdb_1ueb
Previous IDs: none
Type: Domain
Author: Sammut SJ
Number in seed: 108
Number in full: 5622
Average length of the domain: 55.20 aa
Average identity of full alignment: 50 %
Average coverage of the sequence by the domain: 29.52 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 25.2 27.8
Noise cut-off 20.2 23.9
Model length: 56
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

EFP

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 Elong-fact-P_C domain has been found. There are 10 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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