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102  structures 16442  species 5  interactions 23082  sequences 49  architectures

Family: GTP_EFTU_D3 (PF03143)

Summary: Elongation factor Tu C-terminal domain

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This is the Wikipedia entry entitled "GTP-binding elongation factor family, EF-Tu/EF-1A subfamily". More...

GTP-binding elongation factor family, EF-Tu/EF-1A subfamily Edit Wikipedia article

Elongation factor Tu GTP binding domain
PDB 1s0u EBI.jpg
eif2gamma apo
Identifiers
Symbol GTP_EFTU
Pfam PF00009
Pfam clan CL0023
InterPro IPR000795
PROSITE PDOC00273
SCOP 1etu
SUPERFAMILY 1etu
Elongation factor Tu domain 2
PDB 1s0u EBI.jpg
eif2gamma apo
Identifiers
Symbol GTP_EFTU_D2
Pfam PF03144
InterPro IPR004161
PROSITE PDOC00273
SCOP 1etu
SUPERFAMILY 1etu
Elongation factor Tu C-terminal domain
PDB 1dg1 EBI.jpg
whole, unmodified, ef-tu(elongation factor tu).
Identifiers
Symbol GTP_EFTU_D3
Pfam PF03143
InterPro IPR004160
SCOP 1etu
SUPERFAMILY 1etu

In molecular biology, the GTP-binding elongation factor family, EF-Tu/EF-1A subfamily is a family of elongation factors, which includes the eukaryotic eEF-1 and the prokaryotic EF-Tu.

These proteins consist of three structural domains: the GTP-binding domain, and two oligonucleotide binding domains that are often referred to as domain 2 and domain 3.

The GTP-binding domain has been shown [1] to be involved in a conformational change mediated by the hydrolysis of GTP to GDP. This region is conserved in both EF-1alpha/EF-Tu and also in EF-2/EF-G and thus seems typical for GTP-dependent proteins which bind non-initiator tRNAs to the ribosome. The GTP-binding protein synthesis factor family also includes the eukaryotic peptide chain release factor GTP-binding subunits [2] and prokaryotic peptide chain release factor 3 (RF-3);[3] the prokaryotic GTP-binding protein lepA and its homologue in yeast (GUF1) and Caenorhabditis elegans (ZK1236.1); yeast HBS1;[4] rat statin S1;[5] and the prokaryotic selenocysteine-specific elongation factor selB.[6]

Domain 2 adopts a beta-barrel structure, and is involved in binding to charged tRNA.[7] This domain is structurally related to the C-terminal domain of EF2, to which it displays weak sequence similarity. This domain is also found in other proteins such as translation initiation factor IF-2 and tetracycline-resistance proteins.

Domain 3 represents the C-terminal domain, which adopts a beta-barrel structure, and is involved in binding to both charged tRNA and to EF1B (or EF-Ts).[8]

References

  1. ^ Moller W, Schipper A, Amons R (September 1987). "A conserved amino acid sequence around Arg-68 of Artemia elongation factor 1 alpha is involved in the binding of guanine nucleotides and aminoacyl transfer RNAs". Biochimie 69 (9): 983–9. doi:10.1016/0300-9084(87)90232-X. PMID 3126836. 
  2. ^ Stansfield I, Jones KM, Kushnirov VV, Dagkesamanskaya AR, Poznyakovski AI, Paushkin SV, Nierras CR, Cox BS, Ter-Avanesyan MD, Tuite MF (September 1995). "The products of the SUP45 (eRF1) and SUP35 genes interact to mediate translation termination in Saccharomyces cerevisiae". EMBO J. 14 (17): 4365–73. PMC 394521. PMID 7556078. 
  3. ^ Grentzmann G, Brechemier-Baey D, Heurgué-Hamard V, Buckingham RH (May 1995). "Function of polypeptide chain release factor RF-3 in Escherichia coli. RF-3 action in termination is predominantly at UGA-containing stop signals". J. Biol. Chem. 270 (18): 10595–600. doi:10.1074/jbc.270.18.10595. PMID 7737996. 
  4. ^ Nelson RJ, Ziegelhoffer T, Nicolet C, Werner-Washburne M, Craig EA (October 1992). "The translation machinery and 70 kd heat shock protein cooperate in protein synthesis". Cell 71 (1): 97–105. doi:10.1016/0092-8674(92)90269-I. PMID 1394434. 
  5. ^ Ann DK, Moutsatsos IK, Nakamura T, Lin HH, Mao PL, Lee MJ, Chin S, Liem RK, Wang E (June 1991). "Isolation and characterization of the rat chromosomal gene for a polypeptide (pS1) antigenically related to statin". J. Biol. Chem. 266 (16): 10429–37. PMID 1709933. 
  6. ^ Forchhammer K, Leinfelder W, Bock A (November 1989). "Identification of a novel translation factor necessary for the incorporation of selenocysteine into protein". Nature 342 (6248): 453–6. doi:10.1038/342453a0. PMID 2531290. 
  7. ^ Nissen P, Kjeldgaard M, Thirup S, Polekhina G, Reshetnikova L, Clark BF, Nyborg J (December 1995). "Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog". Science 270 (5241): 1464–72. doi:10.1126/science.270.5241.1464. PMID 7491491. 
  8. ^ Wang Y, Jiang Y, Meyering-Voss M, Sprinzl M, Sigler PB (August 1997). "Crystal structure of the EF-Tu.EF-Ts complex from Thermus thermophilus". Nat. Struct. Biol. 4 (8): 650–6. doi:10.1038/nsb0897-650. PMID 9253415. 

This article incorporates text from the public domain Pfam and InterPro IPR000795

This article incorporates text from the public domain Pfam and InterPro IPR004161

This article incorporates text from the public domain Pfam and InterPro IPR004160

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 Tu C-terminal domain Provide feedback

Elongation factor Tu consists of three structural domains, this is the third domain. This domain adopts a beta barrel structure. This the third domain is involved in binding to both charged tRNA [1] and binding to EF-Ts PF00889 [2].

Literature references

  1. Nissen P, Kjeldgaard M, Thirup S, Polekhina G, Reshetnikova L, Clark BF, Nyborg J; , Science 1995;270:1464-1472.: Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog. PUBMED:7491491 EPMC:7491491

  2. Wang Y, Jiang Y, Meyering-Voss M, Sprinzl M, Sigler PB; , Nat Struct Biol 1997;4:650-656.: Crystal structure of the EF-Tu.EF-Ts complex from Thermus thermophilus. PUBMED:9253415 EPMC:9253415


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004160

Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [PUBMED:12762045, PUBMED:15922593, PUBMED:12932732]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution.

EF1A (also known as EF-1alpha or EF-Tu) is a G-protein. It forms a ternary complex of EF1A-GTP-aminoacyltRNA. The binding of aminoacyl-tRNA stimulates GTP hydrolysis by EF1A, causing a conformational change in EF1A that causes EF1A-GDP to detach from the ribosome, leaving the aminoacyl-tRNA attached at the A-site. Only the cognate aminoacyl-tRNA can induce the required conformational change in EF1A through its tight anticodon-codon binding [PUBMED:15680978, PUBMED:12102560]. EF1A-GDP is returned to its active state, EF1A-GTP, through the action of another elongation factor, EF1B (also known as EF-Ts or EF-1beta/gamma/delta).

EF1A consists of three structural domains. This entry represents the C-terminal domain, which adopts a beta-barrel structure, and is involved in binding to both charged tRNA and to EF1B (or EF-Ts, INTERPRO) [PUBMED:9253415].

More information about these proteins can be found at Protein of the Month: Elongation Factors [PUBMED:].

Gene Ontology

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Domain organisation

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Alignments

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  Seed
(82)
Full
(23082)
Representative proteomes NCBI
(18678)
Meta
(2585)
RP15
(948)
RP35
(1617)
RP55
(2282)
RP75
(2870)
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  Seed
(82)
Full
(23082)
Representative proteomes NCBI
(18678)
Meta
(2585)
RP15
(948)
RP35
(1617)
RP55
(2282)
RP75
(2870)
Alignment:
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  Seed
(82)
Full
(23082)
Representative proteomes NCBI
(18678)
Meta
(2585)
RP15
(948)
RP35
(1617)
RP55
(2282)
RP75
(2870)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

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Curation and family details

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Curation View help on the curation process

Seed source: PF00009
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 82
Number in full: 23082
Average length of the domain: 86.00 aa
Average identity of full alignment: 47 %
Average coverage of the sequence by the domain: 25.05 %

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 21.3 7.1
Trusted cut-off 21.3 8.4
Noise cut-off 21.2 -1000000.0
Model length: 99
Family (HMM) version: 12
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Species distribution

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Interactions

There are 5 interactions for this family. More...

EF_TS EF1_GNE GTP_EFTU_D3 GTP_EFTU_D2 GTP_EFTU

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 GTP_EFTU_D3 domain has been found. There are 102 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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