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215  structures 8732  species 0  interactions 21227  sequences 232  architectures

Family: GTP_EFTU_D3 (PF03143)

Summary: Elongation factor Tu C-terminal domain

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This is the Wikipedia entry entitled "EF-Tu". More...

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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
SymbolGTP_EFTU
PfamPF00009
Pfam clanCL0023
InterProIPR000795
PROSITEPDOC00273
SCOP21etu / SCOPe / SUPFAM
Elongation factor Tu domain 2
PDB 1s0u EBI.jpg
eif2gamma apo
Identifiers
SymbolGTP_EFTU_D2
PfamPF03144
InterProIPR004161
PROSITEPDOC00273
SCOP21etu / SCOPe / SUPFAM
Elongation factor Tu C-terminal domain
PDB 1dg1 EBI.jpg
whole, unmodified, ef-tu(elongation factor tu).
Identifiers
SymbolGTP_EFTU_D3
PfamPF03143
InterProIPR004160
SCOP21etu / SCOPe / SUPFAM

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, 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 (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. PMID 3126836. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  2. ^ Stansfield I, Jones KM, Kushnirov VV, Dagkesamanskaya AR, Poznyakovski AI, Paushkin SV, Nierras CR, Cox BS, Ter-Avanesyan MD, Tuite MF (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. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  3. ^ Grentzmann G, Brechemier-Baey D, Heurgué-Hamard V, Buckingham RH (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. PMID 7737996. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  4. ^ Nelson RJ, Ziegelhoffer T, Nicolet C, Werner-Washburne M, Craig EA (1992). "The translation machinery and 70 kd heat shock protein cooperate in protein synthesis". Cell. 71 (1): 97–105. PMID 1394434. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  5. ^ Ann DK, Moutsatsos IK, Nakamura T, Lin HH, Mao PL, Lee MJ, Chin S, Liem RK, Wang E (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. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  6. ^ Forchhammer K, Leinfelder W, Bock A (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. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  7. ^ Nissen P, Kjeldgaard M, Thirup S, Polekhina G, Reshetnikova L, Clark BF, Nyborg J (1995). "Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog". Science. 270 (5241): 1464–72. PMID 7491491. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  8. ^ Wang Y, Jiang Y, Meyering-Voss M, Sprinzl M, Sigler PB (1997). "Crystal structure of the EF-Tu.EF-Ts complex from Thermus thermophilus". Nat. Struct. Biol. 4 (8): 650–6. PMID 9253415. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
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


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004160

Elongation factor EF1A (also known as EF-1alpha or EF-Tu) promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. EF1A consists of three structural domains. Release factor eRF3, which governs translation termination, has a similar overall structure. RF3 has an N-terminal extension and a EF1A-like C-terminal region which comprises a GTP-binding domain (G domain) and two beta-barrel domains that are similar to the three respective domains of elongation factor EF-Tu/eEF1A [ PUBMED:10676813 ]. Archaeal EF1A is both involved in translational elongation and termination, as well as in mRNA surveillance, which explains the lack of an eRF3 orthologue in archaea [ PUBMED:20974926 ].

This entry represents the C-terminal domain of both EF1A and eRF3, which adopts a beta-barrel structure. In EF1A, this domain is involved in binding to both charged tRNA and to EF1B (or EF-Ts, INTERPRO ) [ PUBMED:9253415 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

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 and the UniProtKB sequence database. More...

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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
(50)
Full
(21227)
Representative proteomes UniProt
(108713)
RP15
(3537)
RP35
(9972)
RP55
(19082)
RP75
(29432)
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PP/heatmap 1            

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  Seed
(50)
Full
(21227)
Representative proteomes UniProt
(108713)
RP15
(3537)
RP35
(9972)
RP55
(19082)
RP75
(29432)
Alignment:
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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
(50)
Full
(21227)
Representative proteomes UniProt
(108713)
RP15
(3537)
RP35
(9972)
RP55
(19082)
RP75
(29432)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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 View help on the curation process

Seed source: PF00009
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 50
Number in full: 21227
Average length of the domain: 98.6 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 22.19 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.7 7.3
Trusted cut-off 24.7 7.6
Noise cut-off 24.6 7.2
Model length: 108
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
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Viroids Viroids Unclassified sequence Unclassified sequence

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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 215 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.

Protein Predicted structure External Information
A0A044RGS6 View 3D Structure Click here
A0A044RJK1 View 3D Structure Click here
A0A044TY02 View 3D Structure Click here
A0A077YYL7 View 3D Structure Click here
A0A077Z6Y4 View 3D Structure Click here
A0A077ZEB1 View 3D Structure Click here
A0A077ZH99 View 3D Structure Click here
A0A077ZHW7 View 3D Structure Click here
A0A077ZIE3 View 3D Structure Click here
A0A096MJE3 View 3D Structure Click here
A0A0A2V2X4 View 3D Structure Click here
A0A0D2EIA2 View 3D Structure Click here
A0A0D2GDK8 View 3D Structure Click here
A0A0D2H0C1 View 3D Structure Click here
A0A0D2HPE5 View 3D Structure Click here
A0A0G2KAQ4 View 3D Structure Click here
A0A0H3GLP8 View 3D Structure Click here
A0A0H5SCL8 View 3D Structure Click here
A0A0J9XWD8 View 3D Structure Click here
A0A0K0E303 View 3D Structure Click here
A0A0K0EET9 View 3D Structure Click here
A0A0K0EF94 View 3D Structure Click here
A0A0K0EJY8 View 3D Structure Click here
A0A0K0JGH4 View 3D Structure Click here
A0A0K0JHW8 View 3D Structure Click here
A0A0N4U5V4 View 3D Structure Click here
A0A0N4UFA1 View 3D Structure Click here
A0A0N4UFA5 View 3D Structure Click here
A0A0N4UFM5 View 3D Structure Click here
A0A0N4UJM6 View 3D Structure Click here
A0A0N4UNM4 View 3D Structure Click here
A0A0N7KIR1 View 3D Structure Click here
A0A0P0UXG8 View 3D Structure Click here
A0A0R0ESZ8 View 3D Structure Click here
A0A0R0EV63 View 3D Structure Click here
A0A0R0FCD2 View 3D Structure Click here
A0A0R0FER5 View 3D Structure Click here
A0A0R0FKF0 View 3D Structure Click here
A0A0R0FM97 View 3D Structure Click here
A0A0R0JTV5 View 3D Structure Click here