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694  structures 9117  species 0  interactions 95606  sequences 821  architectures

Family: GTP_EFTU (PF00009)

Summary: Elongation factor Tu GTP binding 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 "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 GTP binding domain Provide feedback

This domain contains a P-loop motif, also found in several other families such as PF00071 PF00025 and PF00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains.

Literature references

  1. Stark H, Rodnina MV, Rinke-Appel J, Brimacombe R, Wintermeyer W, van Heel M; , Nature 1997;389:403-406.: Visualization of elongation factor Tu on the Escherichia coli ribosome. PUBMED:9311785 EPMC:9311785


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000795

Translational GTPases (trGTPases) are a family of proteins in which GTPase activity is stimulated by the large ribosomal subunit. This family includes translation initiation, elongation, and release factors and contains four subfamilies that are widespread, if not ubiquitous, in all three superkingdoms [ PUBMED:11916378 ]. The trGTPase family members include bacteria elongation factors, EFTu, EFG, and the initiation factor, IF2, and their archaeal homologues, the EF1, EF2, aeIF5b and aeIF2. They all contain two homologous N-terminal domains: a GTPase or G-domain, followed by an OB-domain. These translational proteins' G-domains are both structurally and functionally related to a larger family of GTPase G proteins [ PUBMED:11916378 ]. This entry represents the G-domain of the trGTPases.

The basic topology of the tr-type G domain consists of a six-stranded central beta-sheet surrounded by five alpha-helices. Helices alpha2, alpha3 and alpha4 are on one side of the sheet, whereas alpha1 and alpha5 are on the other [ PUBMED:15616587 ]. GTP is bound by the CTF-type G domain in a way common for G domains involving five conserved sequence motifs termed G1-G5. The base is in contact with the NKxD (G4) and SAx (G5) motifs, and the phosphates of the nucleotide are stabilized by main- and side-chain interactions with the P loop GxxxxGKT (G1). The most severe conformational changes are observed for the two switch regions which contain the xT/Sx (G2) and DxxG (G3) motifs that function as sensors for the presence of the gamma-phosphate. A Mg(2+) ion is coordinated by six oxygen ligands with octahedral coordination geometry; two of the ligands are water molecules, two come from the beta- and gamma- phosphates, and two are provided by the side chains of G1 and G2 threonines [ PUBMED:24686316 ].

In both prokaryotes and eukaryotes, there are three distinct types of elongation factors, EF-1alpha (EF-Tu), which binds GTP and an aminoacyl-tRNA and delivers the latter to the A site of ribosomes; EF-1beta (EF-Ts), which interacts with EF-1a/EF-Tu to displace GDP and thus allows the regeneration of GTP-EF-1a; and EF-2 (EF-G), which binds GTP and peptidyl-tRNA and translocates the latter from the A site to the P site. In EF-1-alpha, a specific region has been shown [ PUBMED:3126836 ] 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 as well as 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 [ PUBMED:7556078 ] and prokaryotic peptide chain release factor 3 (RF-3) [ PUBMED:7737996 ]; the prokaryotic GTP-binding protein lepA and its homologue in yeast (GUF1) and Caenorhabditis elegans (ZK1236.1); yeast HBS1 [ PUBMED:1394434 ]; rat statin S1 [ PUBMED:1709933 ]; and the prokaryotic selenocysteine-specific elongation factor selB [ PUBMED:2531290 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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

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Pfam Clan

This family is a member of clan P-loop_NTPase (CL0023), which has the following description:

AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].

The clan contains the following 245 members:

6PF2K AAA AAA-ATPase_like AAA_10 AAA_11 AAA_12 AAA_13 AAA_14 AAA_15 AAA_16 AAA_17 AAA_18 AAA_19 AAA_2 AAA_21 AAA_22 AAA_23 AAA_24 AAA_25 AAA_26 AAA_27 AAA_28 AAA_29 AAA_3 AAA_30 AAA_31 AAA_32 AAA_33 AAA_34 AAA_35 AAA_5 AAA_6 AAA_7 AAA_8 AAA_9 AAA_PrkA ABC_ATPase ABC_tran ABC_tran_Xtn Adeno_IVa2 Adenylsucc_synt ADK AFG1_ATPase AIG1 APS_kinase Arf ArsA_ATPase ATP-synt_ab ATP_bind_1 ATP_bind_2 ATPase ATPase_2 Bac_DnaA BCA_ABC_TP_C Beta-Casp bpMoxR BrxC_BrxD BrxL_ATPase Cas_Csn2 Cas_St_Csn2 CbiA CBP_BcsQ CDC73_C CENP-M CFTR_R CLP1_P CMS1 CoaE CobA_CobO_BtuR CobU cobW CPT CSM2 CTP_synth_N Cytidylate_kin Cytidylate_kin2 DAP3 DEAD DEAD_2 divDNAB DLIC DNA_pack_C DNA_pack_N DNA_pol3_delta DNA_pol3_delta2 DnaB_C dNK DO-GTPase1 DO-GTPase2 DUF1611 DUF2075 DUF2326 DUF2478 DUF257 DUF2813 DUF3584 DUF463 DUF4914 DUF5906 DUF6079 DUF815 DUF835 DUF87 DUF927 Dynamin_N Dynein_heavy Elong_Iki1 ELP6 ERCC3_RAD25_C Exonuc_V_gamma FeoB_N Fer4_NifH Flavi_DEAD FTHFS FtsK_SpoIIIE G-alpha Gal-3-0_sulfotr GBP GBP_C GpA_ATPase GpA_nuclease GTP_EFTU Gtr1_RagA Guanylate_kin GvpD_P-loop HDA2-3 Helicase_C Helicase_C_2 Helicase_C_4 Helicase_RecD HerA_C Herpes_Helicase Herpes_ori_bp Herpes_TK HydF_dimer HydF_tetramer Hydin_ADK IIGP IPPT IPT iSTAND IstB_IS21 KAP_NTPase KdpD Kinase-PPPase Kinesin KTI12 LAP1_C LpxK MCM MeaB MEDS Mg_chelatase Microtub_bd MipZ MMR_HSR1 MMR_HSR1_C MobB MukB Mur_ligase_M MutS_V Myosin_head NACHT NAT_N NB-ARC NOG1 NTPase_1 NTPase_P4 ORC3_N P-loop_TraG ParA Parvo_NS1 PAXNEB PduV-EutP PhoH PIF1 Ploopntkinase1 Ploopntkinase2 Ploopntkinase3 Podovirus_Gp16 Polyoma_lg_T_C Pox_A32 PPK2 PPV_E1_C PRK PSY3 Rad17 Rad51 Ras RecA ResIII RHD3_GTPase RhoGAP_pG1_pG2 RHSP RNA12 RNA_helicase Roc RsgA_GTPase RuvB_N SbcC_Walker_B SecA_DEAD Senescence Septin Sigma54_activ_2 Sigma54_activat SKI SMC_N SNF2-rel_dom SpoIVA_ATPase Spore_III_AA SRP54 SRPRB SulA Sulfotransfer_1 Sulfotransfer_2 Sulfotransfer_3 Sulfotransfer_4 Sulfotransfer_5 Sulphotransf SWI2_SNF2 T2SSE T4SS-DNA_transf TerL_ATPase Terminase_3 Terminase_6N Thymidylate_kin TIP49 TK TmcA_N TniB Torsin TraG-D_C tRNA_lig_kinase TrwB_AAD_bind TsaE UvrB UvrD-helicase UvrD_C UvrD_C_2 Viral_helicase1 VirC1 VirE YqeC Zeta_toxin Zot

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
(142)
Full
(95606)
Representative proteomes UniProt
(452895)
RP15
(15527)
RP35
(46012)
RP55
(90201)
RP75
(145733)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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  Seed
(142)
Full
(95606)
Representative proteomes UniProt
(452895)
RP15
(15527)
RP35
(46012)
RP55
(90201)
RP75
(145733)
Alignment:
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  Seed
(142)
Full
(95606)
Representative proteomes UniProt
(452895)
RP15
(15527)
RP35
(46012)
RP55
(90201)
RP75
(145733)
Raw Stockholm Download   Download   Download   Download   Download      
Gzipped 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: Prosite
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 142
Number in full: 95606
Average length of the domain: 224.7 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 35.43 %

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 26.5 26.5
Trusted cut-off 26.5 26.5
Noise cut-off 26.4 26.4
Model length: 195
Family (HMM) version: 30
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
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 domain has been found. There are 694 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
A0A044REP1 View 3D Structure Click here
A0A044RGS6 View 3D Structure Click here
A0A044RJK1 View 3D Structure Click here
A0A044RZ79 View 3D Structure Click here
A0A044TNR6 View 3D Structure Click here
A0A044TY02 View 3D Structure Click here
A0A044UDB9 View 3D Structure Click here
A0A044UHR8 View 3D Structure Click here
A0A044UJF6 View 3D Structure Click here
A0A044UNP0 View 3D Structure Click here
A0A044V0R1 View 3D Structure Click here
A0A044V4A5 View 3D Structure Click here
A0A044V8P4 View 3D Structure Click here
A0A077YYL7 View 3D Structure Click here
A0A077Z0M0 View 3D Structure Click here
A0A077Z2B6 View 3D Structure Click here
A0A077Z4G7 View 3D Structure Click here
A0A077Z6J6 View 3D Structure Click here
A0A077Z6Y4 View 3D Structure Click here
A0A077Z7P3 View 3D Structure Click here
A0A077Z806 View 3D Structure Click here
A0A077Z966 View 3D Structure Click here
A0A077ZBD6 View 3D Structure Click here
A0A077ZBR8 View 3D Structure Click here
A0A077ZCC1 View 3D Structure Click here
A0A077ZDZ9 View 3D Structure Click here
A0A077ZE73 View 3D Structure Click here
A0A077ZEB1 View 3D Structure Click here
A0A077ZEN1 View 3D Structure Click here
A0A077ZG10 View 3D Structure Click here
A0A077ZGW3 View 3D Structure Click here
A0A077ZHL8 View 3D Structure Click here
A0A077ZHW7 View 3D Structure Click here
A0A077ZIE3 View 3D Structure Click here
A0A077ZKN4 View 3D Structure Click here
A0A077ZL10 View 3D Structure Click here
A0A077ZL12 View 3D Structure Click here
A0A077ZL28 View 3D Structure Click here
A0A096MJE3 View 3D Structure Click here
A0A096QR66 View 3D Structure Click here