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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

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

EF-Tu Edit Wikipedia article

Elongation Factor Thermo Unstable
081-EF-Tu-1ttt.jpg
EF-Tu (blue) complexed with tRNA (red) and GTP (yellow) [1]
Identifiers
SymbolEF-Tu
PfamGTP_EFTU
Pfam clanCL0023
InterProIPR004541
PROSITEPDOC00273
CATH1ETU
SCOP21ETU / SCOPe / SUPFAM
CDDcd00881
EF-Tu
Identifiers
SymbolGTP_EFTU_D2
PfamPF03144
InterProIPR004161
CDDcd01342
Elongation factor Tu domain 3
Identifiers
SymbolGTP_EFTU_D3
PfamPF03143
InterProIPR004160
CDDcd01513

EF-Tu (elongation factor thermo unstable) is a prokaryotic elongation factor responsible for catalyzing the binding of an aminoacyl-tRNA (aa-tRNA) to the ribosome. It is a G-protein, and facilitates the selection and binding of an aa-tRNA to the A-site of the ribosome. As a reflection of its crucial role in translation, EF-Tu is one of the most abundant and highly conserved proteins in prokaryotes.[2][3][4] It is found in eukaryotic mitochrondria as TUFM.[5]

As a family of elongation factors, EF-Tu also includes its eukaryotic and archaeal homolog, the alpha subunit of eEF-1 (EF-1A).

Background

Elongation factors are part of the mechanism that synthesizes new proteins through translation in the ribosome. Transfer RNAs (tRNAs) carry the individual amino acids that become integrated into a protein sequence, and have an anticodon for the specific amino acid that they are charged with. Messenger RNA (mRNA) carries the genetic information that encodes the primary structure of a protein, and contains codons that code for each amino acid. The ribosome creates the protein chain by following the mRNA code and integrating the amino acid of an aminoacyl-tRNA (also known as a charged tRNA) to the growing polypeptide chain.[6][7]

There are three sites on the ribosome for tRNA binding. These are the aminoacyl/acceptor site (abbreviated A), the peptidyl site (abbreviated P), and the exit site (abbreviated E). The P-site holds the tRNA connected to the polypeptide chain being synthesized, and the A-site is the binding site for a charged tRNA with an anticodon complementary to the mRNA codon associated with the site. After binding of a charged tRNA to the A-site, a peptide bond is formed between the growing polypeptide chain on the P-site tRNA and the amino acid of the A-site tRNA, and the entire polypeptide is transferred from the P-site tRNA to the A-site tRNA. Then, in a process catalyzed by the prokaryotic elongation factor EF-G (historically known as translocase), the coordinated translocation of the tRNAs and mRNA occurs, with the P-site tRNA moving to the E-site, where it dissociates from the ribosome, and the A-site tRNA moves to take its place in the P-site.[6][7]

Biological functions

The cyclical role of EF-Tu in translation. Structures are from PDBs 1EFT, 1TUI, and 1TTT.

Protein synthesis

EF-Tu participates in the polypeptide elongation process of protein synthesis. In prokaryotes, the primary function of EF-Tu is to transport the correct aa-tRNA to the A-site of the ribosome. As a G-protein, it uses GTP to facilitate its function. Outside of the ribosome, EF-Tu complexed with GTP (EF-Tu • GTP) complexes with aa-tRNA to form a stable EF-Tu • GTP • aa-tRNA ternary complex.[8] EF-Tu • GTP binds all correctly-charged aa-tRNAs with approximately identical affinity, except those charged with initiation residues and selenocysteine.[9][10] This can be accomplished because although different amino acid residues have varying side-chain properties, the tRNAs associated with those residues have varying structures to compensate for differences in side-chain binding affinities.[11][12]

The binding of an aa-tRNA to EF-Tu • GTP allows for the ternary complex to be translocated to the A-site of an active ribosome, in which the anticodon of the tRNA binds to the codon of the mRNA. If the correct anticodon binds to the mRNA codon, the ribosome changes configuration and alters the geometry of the GTPase domain of EF-Tu, resulting in the hydrolysis of the GTP associated with the EF-Tu to GDP and Pi. As such, the ribosome functions as a GTPase-activating protein (GAP) for EF-Tu. Upon GTP hydrolysis, the conformation of EF-Tu changes drastically and dissociates from the aa-tRNA and ribosome complex.[4][13] The aa-tRNA then fully enters the A-site, where its amino acid is brought near the P-site's polypeptide and the ribosome catalyzes the covalent transfer of the polypeptide onto the amino acid.[10]

In the cytoplasm, the deactivated EF-Tu • GDP is acted on by the prokaryotic elongation factor EF-Ts, which causes EF-Tu to release its bound GDP. Upon dissociation of EF-Ts, EF-Tu is able to complex with a GTP due to the 5– to 10–fold higher concentration of GTP than GDP in the cytoplasm, resulting in reactivated EF-Tu • GTP, which can then associate with another aa-tRNA.[8][13]

Maintaining translational accuracy

EF-Tu contributes to translational accuracy in three ways. In translation, a fundamental problem is that near-cognate anticodons have similar binding affinity to a codon as cognate anticodons, such that anticodon-codon binding in the ribosome alone is not sufficient to maintain high translational fidelity. This is addressed by the ribosome not activating the GTPase activity of EF-Tu if the tRNA in the ribosome's A-site does not match the mRNA codon, thus preferentially increasing the likelihood for the incorrect tRNA to leave the ribosome.[14] Additionally, regardless of tRNA matching, EF-Tu also induces a delay after freeing itself from the aa-tRNA, before the aa-tRNA fully enters the A-site (a process called accommodation). This delay period is a second opportunity for incorrectly charged aa-tRNAs to move out of the A-site before the incorrect amino acid is irreversibly added to the polypeptide chain.[15][16] A third mechanism is the less well understood function of EF-Tu to crudely check aa-tRNA associations and reject complexes where the amino acid is not bound to the correct tRNA coding for it.[11]

Other functions

EF-Tu has been found in large quantities in the cytoskeletons of bacteria, co-localizing underneath the cell membrane with MreB, a cytoskeletal element that maintains cell shape.[17][18] Defects in EF-Tu have been shown to result in defects in bacterial morphology.[19] Additionally, EF-Tu has displayed some chaperone-like characteristics, with some experimental evidence suggesting that it promotes the refolding of a number of denatured proteins in vitro.[20][21]

Structure

EF-Tu bound to GDP (yellow) and GDPNP (red), a GTP-like molecule. The GTPase domain (domain I) of EF-Tu is depicted in dark blue, while the oligonucleotide-binding domains II and III are depicted in light blue. Structures are from PDBs 1EFT and 1TUI, for GDP- and GDPNP-bound EF-Tu, respectively.

EF-Tu is a monomeric protein with molecular weight around 43 kDa in Escherichia coli.[22][23][24] The protein consists of three structural domains: a GTP-binding domain and two oligonucleotide-binding domains, often referred to as domain 2 and domain 3. The N-terminal domain I of EF-Tu is the GTP-binding domain. It consists of a six beta-strand core flanked by six alpha-helices.[8] Domains II and III of EF-Tu, the oligonucleotide-binding domains, both adopt beta-barrel structures.[25][26]

The GTP-binding domain I undergoes a dramatic conformational change upon GTP hydrolysis to GDP, allowing EF-Tu to dissociate from aa-tRNA and leave the ribosome.[27] Reactivation of EF-Tu is achieved by GTP binding in the cytoplasm, which leads to a significant conformational change that reactivates the tRNA-binding site of EF-Tu. In particular, GTP binding to EF-Tu results in a ~90° rotation of domain I relative to domains II and III, exposing the residues of the tRNA-binding active site.[28]

Domain 2 adopts a beta-barrel structure, and is involved in binding to charged tRNA.[29] 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).[30]

Evolution

The GTP-binding domain 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[31] and prokaryotic peptide chain release factor 3 (RF-3);[32] the prokaryotic GTP-binding protein lepA and its homologue in yeast (GUF1) and Caenorhabditis elegans (ZK1236.1); yeast HBS1;[33] rat statin S1;[34] and the prokaryotic selenocysteine-specific elongation factor selB.[35]

Disease relevance

Along with the ribosome, EF-Tu is one of the most important targets for antibiotic-mediated inhibition of translation.[8] Antibiotics targeting EF-Tu can be categorized into one of two groups, depending on the mechanism of action, and one of four structural families. The first group includes the antibiotics pulvomycin and GE2270A, and inhibits the formation of the ternary complex.[36] The second group includes the antibiotics kirromycin and enacyloxin, and prevents the release of EF-Tu from the ribosome after GTP hydrolysis.[37][38][39]

See also

References

  1. ^ PDB Molecule of the Month EF-Tu
  2. ^ Weijland A, Harmark K, Cool RH, Anborgh PH, Parmeggiani A (March 1992). "Elongation factor Tu: a molecular switch in protein biosynthesis". Molecular Microbiology. 6 (6): 683–8. doi:10.1111/j.1365-2958.1992.tb01516.x. PMID 1573997.
  3. ^ "TIGR00485: EF-Tu". National Center for Biotechnology Information. March 3, 2017.
  4. ^ a b Yamamoto H, Qin Y, Achenbach J, Li C, Kijek J, Spahn CM, Nierhaus KH (February 2014). "EF-G and EF4: translocation and back-translocation on the bacterial ribosome". Nature Reviews. Microbiology. 12 (2): 89–100. doi:10.1038/nrmicro3176. PMID 24362468. S2CID 27196901.
  5. ^ Ling M, Merante F, Chen HS, Duff C, Duncan AM, Robinson BH (Nov 1997). "The human mitochondrial elongation factor tu (EF-Tu) gene: cDNA sequence, genomic localization, genomic structure, and identification of a pseudogene". Gene. 197 (1–2): 325–36. doi:10.1016/S0378-1119(97)00279-5. PMID 9332382.
  6. ^ a b Laursen BS, Sørensen HP, Mortensen KK, Sperling-Petersen HU (March 2005). "Initiation of protein synthesis in bacteria". Microbiology and Molecular Biology Reviews. 69 (1): 101–23. doi:10.1128/MMBR.69.1.101-123.2005. PMC 1082788. PMID 15755955.
  7. ^ a b Ramakrishnan V (February 2002). "Ribosome structure and the mechanism of translation". Cell. 108 (4): 557–72. doi:10.1016/s0092-8674(02)00619-0. PMID 11909526. S2CID 2078757.
  8. ^ a b c d Krab IM, Parmeggiani A (2002-01-01). Mechanisms of EF-Tu, a pioneer GTPase. Progress in Nucleic Acid Research and Molecular Biology. 71. pp. 513–51. doi:10.1016/S0079-6603(02)71050-7. ISBN 9780125400718. PMID 12102560.
  9. ^ "Translation elongation factor EFTu/EF1A, bacterial/organelle (IPR004541)". InterPro.
  10. ^ a b Diwan, Joyce (2008). "Translation: Protein Synthesis". Rensselaer Polytechnic Institute.
  11. ^ a b LaRiviere FJ, Wolfson AD, Uhlenbeck OC (October 2001). "Uniform binding of aminoacyl-tRNAs to elongation factor Tu by thermodynamic compensation". Science. 294 (5540): 165–8. doi:10.1126/science.1064242. PMID 11588263. S2CID 26192336.
  12. ^ Louie A, Ribeiro NS, Reid BR, Jurnak F (April 1984). "Relative affinities of all Escherichia coli aminoacyl-tRNAs for elongation factor Tu-GTP". The Journal of Biological Chemistry. 259 (8): 5010–6. doi:10.1016/S0021-9258(17)42947-4. PMID 6370998.
  13. ^ a b Clark BF, Nyborg J (February 1997). "The ternary complex of EF-Tu and its role in protein biosynthesis". Current Opinion in Structural Biology. 7 (1): 110–6. doi:10.1016/s0959-440x(97)80014-0. PMID 9032056.
  14. ^ Nilsson J, Nissen P (June 2005). "Elongation factors on the ribosome". Current Opinion in Structural Biology. 15 (3): 349–54. doi:10.1016/j.sbi.2005.05.004. PMID 15922593.
  15. ^ Whitford PC, Geggier P, Altman RB, Blanchard SC, Onuchic JN, Sanbonmatsu KY (June 2010). "Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways". RNA. 16 (6): 1196–204. doi:10.1261/rna.2035410. PMC 2874171. PMID 20427512.
  16. ^ Noel JK, Whitford PC (October 2016). "How EF-Tu can contribute to efficient proofreading of aa-tRNA by the ribosome". Nature Communications. 7: 13314. doi:10.1038/ncomms13314. PMC 5095583. PMID 27796304.
  17. ^ Defeu Soufo HJ, Reimold C, Linne U, Knust T, Gescher J, Graumann PL (February 2010). "Bacterial translation elongation factor EF-Tu interacts and colocalizes with actin-like MreB protein". Proceedings of the National Academy of Sciences of the United States of America. 107 (7): 3163–8. doi:10.1073/pnas.0911979107. PMC 2840354. PMID 20133608.
  18. ^ Mayer F (2003-01-01). "Cytoskeletons in prokaryotes". Cell Biology International. 27 (5): 429–38. doi:10.1016/s1065-6995(03)00035-0. PMID 12758091. S2CID 40897586.
  19. ^ Mayer F (2006-01-01). "Cytoskeletal elements in bacteria Mycoplasma pneumoniae, Thermoanaerobacterium sp., and Escherichia coli as revealed by electron microscopy". Journal of Molecular Microbiology and Biotechnology. 11 (3–5): 228–43. doi:10.1159/000094057. PMID 16983198. S2CID 23701662.
  20. ^ Richarme G (November 1998). "Protein-disulfide isomerase activity of elongation factor EF-Tu". Biochemical and Biophysical Research Communications. 252 (1): 156–61. doi:10.1006/bbrc.1998.9591. PMID 9813162.
  21. ^ Kudlicki W, Coffman A, Kramer G, Hardesty B (December 1997). "Renaturation of rhodanese by translational elongation factor (EF) Tu. Protein refolding by EF-Tu flexing". The Journal of Biological Chemistry. 272 (51): 32206–10. doi:10.1074/jbc.272.51.32206. PMID 9405422.
  22. ^ Caldas TD, El Yaagoubi A, Kohiyama M, Richarme G (October 1998). "Purification of elongation factors EF-Tu and EF-G from Escherichia coli by covalent chromatography on thiol-sepharose". Protein Expression and Purification. 14 (1): 65–70. doi:10.1006/prep.1998.0922. PMID 9758752.
  23. ^ Wiborg O, Andersen C, Knudsen CR, Clark BF, Nyborg J (August 1996). "Mapping Escherichia coli elongation factor Tu residues involved in binding of aminoacyl-tRNA". The Journal of Biological Chemistry. 271 (34): 20406–11. doi:10.1074/jbc.271.34.20406. PMID 8702777.
  24. ^ Wurmbach P, Nierhaus KH (1979-01-01). Isolation of the protein synthesis elongation factors EF-Tu, EF-Ts, and EF-G from Escherichia coli. Methods in Enzymology. 60. pp. 593–606. doi:10.1016/s0076-6879(79)60056-3. ISBN 9780121819606. PMID 379535.
  25. ^ 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". Nature Structural Biology. 4 (8): 650–6. doi:10.1038/nsb0897-650. PMID 9253415. S2CID 10644042.
  26. ^ 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. S2CID 24817616.
  27. ^ Möller 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.
  28. ^ Kjeldgaard M, Nissen P, Thirup S, Nyborg J (September 1993). "The crystal structure of elongation factor EF-Tu from Thermus aquaticus in the GTP conformation". Structure. 1 (1): 35–50. doi:10.1016/0969-2126(93)90007-4. PMID 8069622.
  29. ^ 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. S2CID 24817616.
  30. ^ 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. S2CID 10644042.
  31. ^ 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. doi:10.1002/j.1460-2075.1995.tb00111.x. PMC 394521. PMID 7556078.
  32. ^ 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.
  33. ^ 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. S2CID 7417370.
  34. ^ 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. doi:10.1016/S0021-9258(18)99243-4. PMID 1709933.
  35. ^ 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. S2CID 4251625.
  36. ^ Selva E, Beretta G, Montanini N, Saddler GS, Gastaldo L, Ferrari P, Lorenzetti R, Landini P, Ripamonti F, Goldstein BP (July 1991). "Antibiotic GE2270 a: a novel inhibitor of bacterial protein synthesis. I. Isolation and characterization". The Journal of Antibiotics. 44 (7): 693–701. doi:10.7164/antibiotics.44.693. PMID 1908853.
  37. ^ Hogg T, Mesters JR, Hilgenfeld R (February 2002). "Inhibitory mechanisms of antibiotics targeting elongation factor Tu". Current Protein & Peptide Science. 3 (1): 121–31. doi:10.2174/1389203023380855. PMID 12370016.
  38. ^ Andersen GR, Nissen P, Nyborg J (August 2003). "Elongation factors in protein biosynthesis". Trends in Biochemical Sciences. 28 (8): 434–41. doi:10.1016/S0968-0004(03)00162-2. PMID 12932732.
  39. ^ Parmeggiani A, Nissen P (August 2006). "Elongation factor Tu-targeted antibiotics: four different structures, two mechanisms of action". FEBS Letters. 580 (19): 4576–81. doi:10.1016/j.febslet.2006.07.039. PMID 16876786. S2CID 20811259.

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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...

View options

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)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(142)
Full
(95606)
Representative proteomes UniProt
(452895)
RP15
(15527)
RP35
(46012)
RP55
(90201)
RP75
(145733)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(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: 224.70 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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Colour assignments

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

Selections

Align selected sequences to HMM

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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The tree shows the occurrence of this domain across different species. More...

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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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
A0A096MJE3 View 3D Structure Click here
A0A096QR66 View 3D Structure Click here
A0A0N7KIR1 View 3D Structure Click here
A0A0N7KJF4 View 3D Structure Click here
A0A0P0UXG8 View 3D Structure Click here
A0A0P0VIM8 View 3D Structure Click here
A0A0P0WNE8 View 3D Structure Click here
A0A0P0XXX9 View 3D Structure Click here
A0A0R0ESZ8 View 3D Structure Click here
A0A0R0F3B5 View 3D Structure Click here
A0A0R0FCD2 View 3D Structure Click here
A0A0R0FER5 View 3D Structure Click here
A0A0R0FM97 View 3D Structure Click here
A0A0R0IEL2 View 3D Structure Click here
A0A0R0JTV5 View 3D Structure Click here
A0A0R0JWG1 View 3D Structure Click here
A0A0R0K0Z8 View 3D Structure Click here
A0A0R0KAP7 View 3D Structure Click here
A0A0R0L7P4 View 3D Structure Click here
A0A0R4ITN4 View 3D Structure Click here
A0A0R4J384 View 3D Structure Click here
A0A0R4J4C3 View 3D Structure Click here
A0A140KXW6 View 3D Structure Click here
A0A1D6DT68 View 3D Structure Click here
A0A1D6E4M0 View 3D Structure Click here
A0A1D6E9T3 View 3D Structure Click here
A0A1D6EEC1 View 3D Structure Click here
A0A1D6EY66 View 3D Structure Click here
A0A1D6FI94 View 3D Structure Click here
A0A1D6FMI2 View 3D Structure Click here
A0A1D6FMY1 View 3D Structure Click here
A0A1D6GD78 View 3D Structure Click here
A0A1D6IGS1 View 3D Structure Click here
A0A1D6J4Q5 View 3D Structure Click here
A0A1D6JDE8 View 3D Structure Click here
A0A1D6KZD6 View 3D Structure Click here
A0A1D6LAW0 View 3D Structure Click here
A0A1D6M1J8 View 3D Structure Click here
A0A1D6MLW3 View 3D Structure Click here
A0A1D6NCM5 View 3D Structure Click here