>gi|91091140|ref|XP_970339.1| PREDICTED: similar to GA19322-PA [Tribolium castaneum] gi|270013130|gb|EFA09578.1| hypothetical protein TcasGA2_TC011692 [Tribolium castaneum]
mtEF-TU is highly conserved and is 55-60% identical to bacterial EF-TU. The overall structure is similar to that observed in the Escherichia coli and Thermus aquaticus EF-TU. However, compared with that observed in prokaryotic EF-TU the nucleotide-binding domain (domain I) of EF-TUmt is in a different orientation relative to the rest of the structure. Furthermore, domain III is followed by a short 11-amino acid extension that forms one helical turn. This extension seems to be specific to the mitochondrial factors and has not been observed in any of the prokaryotic factors. Length = 93
>gnl|CDD|239678 cd03707, EFTU_III, Domain III of elongation factor (EF) Tu
Score = 54.9 bits (133), Expect = 1e-11
Identities = 23/55 (41%), Positives = 31/55 (56%)
Query: 1 MHDHVEAQIYLLTKEEGGRTRPYTPWGQAHVYSKTWDVAARIIDMGGKDMFMPGE 55
H EA++Y+LTKEEGGR P+ + Y +T DV I G +M MPG+
Sbjct: 2 PHTKFEAEVYVLTKEEGGRHTPFFSGYRPQFYIRTTDVTGSITLPEGTEMVMPGD 56
Ef-Tu consists of three structural domains, designated I, II and III. Domain III adopts a beta barrel structure. Domain III is involved in binding to both charged tRNA and binding to elongation factor Ts (EF-Ts). EF-Ts is the guanine-nucleotide-exchange factor for EF-Tu. EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu complexed with GTP and aminoacyl-tRNA delivers tRNA to the ribosome, whereas EF-G stimulates translocation, a process in which tRNA and mRNA movements occur in the ribosome. Crystallographic studies revealed structural similarities ("molecular mimicry") between tertiary structures of EF-G and the EF-Tu-aminoacyl-tRNA ternary complex. Domains III, IV, and V of EF-G mimic the tRNA structure in the EF-Tu ternary complex; domains III, IV and V can be related to the acceptor stem, anticodon helix and T stem of tRNA respectively. Length = 90
>gnl|CDD|217387 pfam03143, GTP_EFTU_D3, Elongation factor Tu C-terminal domain
Score = 52.1 bits (126), Expect = 2e-10
Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 5/54 (9%)
Query: 2 HDHVEAQIYLLTKEEGGRTRPYTPWGQAHVYSKTWDVAARIIDMGGKDMFMPGE 55
H +AQ+Y+L Y P Y T DV + I G K+ MPG+
Sbjct: 5 HTKFKAQVYILNHP-TPIFNGYRP----VFYCHTADVTGKFILPGKKEFVMPGD 53
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 and binding to EF-Ts pfam00889. Length = 91
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu
Score = 46.4 bits (111), Expect = 2e-07
Identities = 24/57 (42%), Positives = 30/57 (52%), Gaps = 8/57 (14%)
Query: 2 HDHVEAQIYLLTKEEGGRTRP----YTPWGQAHVYSKTWDVAARIIDMGGKDMFMPG 54
H EA++Y+L+KEEGGR P Y P Y +T DV I G +M MPG
Sbjct: 304 HTKFEAEVYVLSKEEGGRHTPFFNGYRP----QFYFRTTDVTGTIELPEGVEMVMPG 356
Score = 44.8 bits (106), Expect = 7e-07
Identities = 22/55 (40%), Positives = 31/55 (56%)
Query: 2 HDHVEAQIYLLTKEEGGRTRPYTPWGQAHVYSKTWDVAARIIDMGGKDMFMPGED 56
H EA++Y+L KEEGGR P+ + Y +T DV I G +M MPG++
Sbjct: 302 HTKFEAEVYVLKKEEGGRHTPFFSGYRPQFYFRTTDVTGSITLPEGVEMVMPGDN 356
This model models orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts, one of several GTP-binding translation factors found by the more general pfam model GTP_EFTU. The eukaryotic conterpart, eukaryotic translation elongation factor 1 (eEF-1 alpha), is excluded from this model. EF-Tu is one of the most abundant proteins in bacteria, as well as one of the most highly conserved, and in a number of species the gene is duplicated with identical function. When bound to GTP, EF-Tu can form a complex with any (correctly) aminoacylated tRNA except those for initiation and for selenocysteine, in which case EF-Tu is replaced by other factors. Transfer RNA is carried to the ribosome in these complexes for protein translation [Protein synthesis, Translation factors]. Length = 394
>gnl|CDD|238771 cd01513, Translation_factor_III, Domain III of Elongation factor (EF) Tu (EF-TU) and EF-G
Score = 33.2 bits (76), Expect = 0.004
Identities = 15/67 (22%), Positives = 22/67 (32%), Gaps = 16/67 (23%)
Query: 2 HDHVEAQIYLLTKEEGGRTRPYTPWGQAHVYSKTWDVAARIIDM-----------GGKDM 50
D A+IY+L E P +P + + T V RI + +
Sbjct: 3 VDKFVAEIYVLDHPE-----PLSPGYKPVLNVGTAHVPGRIAKLLSKVDGKTEEKKPPEF 57
Query: 51 FMPGEDG 57
GE G
Sbjct: 58 LKSGERG 64
Elongation factors (EF) EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu complexed with GTP and aminoacyl-tRNA delivers tRNA to the ribosome, whereas EF-G stimulates translocation, a process in which tRNA and mRNA movements occur in the ribosome. Experimental data showed that: (1) intrinsic GTPase activity of EF-G is influenced by excision of its domain III; (2) that EF-G lacking domain III has a 1,000-fold decreased GTPase activity on the ribosome and, a slightly decreased affinity for GTP; and (3) EF-G lacking domain III does not stimulate translocation, despite the physical presence of domain IV which is also very important for translocation. These findings indicate an essential contribution of domain III to activation of GTP hydrolysis. Domains III and V of EF-G have the same fold (although they are not completely superimposable), the double split beta-alpha-beta fold. This fold is observed in a large number of ribonucleotide binding proteins and is also referred to as the ribonucleoprotein (RNP) or RNA recognition (RRM) motif. This domain III is found in several elongation factors, as well as in peptide chain release factors and in GT-1 family of GTPase (GTPBP1). Length = 102
mtEF-TU is highly conserved and is 55-60% identical to bacterial EF-TU. The overall structure is similar to that observed in the Escherichia coli and Thermus aquaticus EF-TU. However, compared with that observed in prokaryotic EF-TU the nucleotide-binding domain (domain I) of EF-TUmt is in a different orientation relative to the rest of the structure. Furthermore, domain III is followed by a short 11-amino acid extension that forms one helical turn. This extension seems to be specific to the mitochondrial factors and has not been observed in any of the prokaryotic factors.
>cd03707 EFTU_III Domain III of elongation factor (EF) Tu
Ef-Tu consists of three structural domains, designated I, II and III. Domain III adopts a beta barrel structure. Domain III is involved in binding to both charged tRNA and binding to elongation factor Ts (EF-Ts). EF-Ts is the guanine-nucleotide-exchange factor for EF-Tu. EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu complexed with GTP and aminoacyl-tRNA delivers tRNA to the ribosome, whereas EF-G stimulates translocation, a process in which tRNA and mRNA movements occur in the ribosome. Crystallographic studies revealed structural similarities ("molecular mimicry") between tertiary structures of EF-G and the EF-Tu-aminoacyl-tRNA ternary complex. Domains III, IV, and V of EF-G mimic the tRNA structure in the EF-Tu ternary complex; domains III, IV and V can be related to the acceptor stem, anticodon helix
>cd04094 selB_III This family represents the domain of elongation factor SelB, homologous to domain III of EF-Tu
SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.
>cd03708 GTPBP_III Domain III of the GP-1 family of GTPase
This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.
>PF03143 GTP_EFTU_D3: Elongation factor Tu C-terminal domain; InterPro: IPR004160 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]
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 [, ]. 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, IPR001816 from INTERPRO) []. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 1TUI_C 1OB5_E 1TTT_B 1B23_P 1EFT_A 3E20_E 1R5B_A 1R5O_A 1R5N_A 3AGJ_C ....
>cd01513 Translation_factor_III Domain III of Elongation factor (EF) Tu (EF-TU) and EF-G
Probab=99.26 E-value=1.7e-11 Score=78.91 Aligned_cols=64 Identities=27% Similarity=0.367 Sum_probs=57.2
Q ss_pred CCceeEEEEEEEecccCCccCCCCCCCeeeEEEecCCeeEEEeecC-----------CceeecCCCCccceE-eeccccc
Q psy9631 1 MHDHVEAQIYLLTKEEGGRTRPYTPWGQAHVYSKTWDVAARIIDMG-----------GKDMFMPGEDGNPDP-LRGPMRP 68 (90)
Q Consensus 1 ~~~kfeAqvYiLtkEEGGR~tPf~~gYrpQff~rT~Dvtg~i~~l~-----------~~~mvMPGD~~~~~v-L~~pm~i 68 (90)
++++|+|+|++|+.++ |+..||++++++.|++++|+|..+. ..++++|||.+.+.+ |.+|+++
T Consensus 2 ~~~~f~a~i~~l~~~~-----pl~~g~~~~l~~~t~~~~~~i~~i~~~~d~~~~~~~~~~~l~~~~~a~v~l~~~~pi~~ 76 (102)
T cd01513 2 AVDKFVAEIYVLDHPE-----PLSPGYKPVLNVGTAHVPGRIAKLLSKVDGKTEEKKPPEFLKSGERGIVEVELQKPVAL 76 (102)
T ss_pred cccEEEEEEEEECCCc-----ccCCCCcEEEEeecCEEeEEEEeeeeecccCcccccCchhhcCCCEEEEEEEECCceEE
Confidence 4689999999999854 9999999999999999999994443 257999999999999 9999998
Q ss_pred c
Q psy9631 69 H 69 (90)
Q Consensus 69 e 69 (90)
|
T Consensus 77 e 77 (102)
T cd01513 77 E 77 (102)
T ss_pred E
Confidence 8
Elongation factors (EF) EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu complexed with GTP and aminoacyl-tRNA delivers tRNA to the ribosome, whereas EF-G stimulates translocation, a process in which tRNA and mRNA movements occur in the ribosome. Experimental data showed that: (1) intrinsic GTPase activity of EF-G is influenced by excision of its domain III; (2) that EF-G lacking domain III has a 1,000-fold decreased GTPase activity on the ribosome and, a slightly decreased affinity for GTP; and (3) EF-G lacking domain III does not stimulate translocation, despite the physical presence of domain IV which is also very important for translocation. These findings indicate an essential contribution of domain III to activation of GTP hydrolysis. Domains III and V of EF-G have the s
>cd03704 eRF3c_III This family represents eEF1alpha-like C-terminal region of eRF3 homologous to the domain III of EF-Tu
eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. The C-terminal region is responsible for translation termination activity and is essential for viability. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-like protein with the property of aggregating into polymer-like fibrils.
This alignment models orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts, one of several GTP-binding translation factors found by the more general pfam model GTP_EFTU. The eukaryotic conterpart, eukaryotic translation elongation factor 1 (eEF-1 alpha), is excluded from this model. EF-Tu is one of the most abundant proteins in bacteria, as well as one of the most highly conserved, and in a number of species the gene is duplicated with identical function. When bound to GTP, EF-Tu can form a complex with any (correctly) aminoacylated tRNA except those for initiation and for selenocysteine, in which case EF-Tu is replaced by other factors. Transfer RNA is carried to the ribosome in these complexes for protein translation.
Eukaryotic elongation factor 1 (EF-1) is responsible for the GTP-dependent binding of aminoacyl-tRNAs to ribosomes. EF-1 is composed of four subunits: the alpha chain, which binds GTP and aminoacyl-tRNAs, the gamma chain that probably plays a role in anchoring the complex to other cellular components and the beta and delta (or beta') chains. This family is the alpha subunit, and represents the counterpart of bacterial EF-Tu for the archaea (aEF-1 alpha) and eukaryotes (eEF-1 alpha).
>cd04093 HBS1_C HBS1_C: this family represents the C-terminal domain of Hsp70 subfamily B suppressor 1 (HBS1) which is homologous to the domain III of EF-1alpha
This group contains proteins similar to yeast Hbs1, a G protein known to be important for efficient growth and protein synthesis under conditions of limiting translation initiation and, to associate with Dom34. It has been speculated that yeast Hbs1 and Dom34 proteins may function as part of a complex with a role in gene expression.
This model represents the counterpart of bacterial EF-Tu for the Archaea (aEF-1 alpha) and Eukaryotes (eEF-1 alpha). The trusted cutoff is set fairly high so that incomplete sequences will score between suggested and trusted cutoff levels.
>cd04095 CysN_NoDQ_III TCysN_NoDQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu
Probab=97.47 E-value=0.00056 Score=44.72 Aligned_cols=63 Identities=17% Similarity=0.220 Sum_probs=52.4
Q ss_pred CceeEEEEEEEecccCCccCCCCCCCeeeEEEecCCeeEEEeecC---C--------ceeecCCCCccceE-eecccccc
Q psy9631 2 HDHVEAQIYLLTKEEGGRTRPYTPWGQAHVYSKTWDVAARIIDMG---G--------KDMFMPGEDGNPDP-LRGPMRPH 69 (90)
Q Consensus 2 ~~kfeAqvYiLtkEEGGR~tPf~~gYrpQff~rT~Dvtg~i~~l~---~--------~~mvMPGD~~~~~v-L~~pm~ie 69 (90)
.++|+|+|-+|.. .|+..||++.+++.|..+.|+|+.+. | -.-+-.||.+.+.+ +.+|+++|
T Consensus 3 ~~~f~a~i~~l~~------~pl~~G~~~~l~~~t~~~~~~i~~i~~~id~~t~~~~~~~~l~~n~~a~v~i~~~~pi~~d 76 (103)
T cd04095 3 SDQFAATLVWMDE------EPLRPGRKYLLKLGTRTVRATVTAIKYRVDVNTLEHEAADTLELNDIGRVELSLSKPLAFD 76 (103)
T ss_pred cceeeEEEEEecC------cccCCCCEEEEEEcCCEEEEEEeeeeEEEcCCCCCccCCCEECCCCeEEEEEEeCCccEec
Confidence 5789999999983 38999999999999999999985541 1 13456699999999 99999988
Q ss_pred c
Q psy9631 70 H 70 (90)
Q Consensus 70 ~ 70 (90)
.
T Consensus 77 ~ 77 (103)
T cd04095 77 P 77 (103)
T ss_pred c
Confidence 6
Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which s
>TIGR02034 CysN sulfate adenylyltransferase, large subunit
Probab=97.31 E-value=0.00055 Score=54.71 Aligned_cols=63 Identities=17% Similarity=0.197 Sum_probs=53.1
Q ss_pred CceeEEEEEEEecccCCccCCCCCCCeeeEEEecCCeeEEEeecC---C--------ceeecCCCCccceE-eecccccc
Q psy9631 2 HDHVEAQIYLLTKEEGGRTRPYTPWGQAHVYSKTWDVAARIIDMG---G--------KDMFMPGEDGNPDP-LRGPMRPH 69 (90)
Q Consensus 2 ~~kfeAqvYiLtkEEGGR~tPf~~gYrpQff~rT~Dvtg~i~~l~---~--------~~mvMPGD~~~~~v-L~~pm~ie 69 (90)
.++|+|++++|.. +|+..||++++++.|..++|+|..+. | .+-+-|||.+.+++ +.+|+++|
T Consensus 306 ~~~f~a~i~~l~~------~~i~~g~~~~l~~gt~~~~~~i~~i~~~~d~~t~~~~~~~~l~~~~~~~v~l~~~~p~~~~ 379 (406)
T TIGR02034 306 ADQFAATLVWMAE------EPLLPGRSYDLKLGTRKVRASVAAIKHKVDVNTLEKGAAKSLELNEIGRVNLSLDEPIAFD 379 (406)
T ss_pred ceEEEEEEEEeCh------hhcCCCCEEEEEeCCCEEEEEEEEEEEEecCCCCcccCCcccCCCCEEEEEEEECCeeccC
Confidence 4689999999973 59999999999999999999994442 1 14566899999999 99999998
Q ss_pred c
Q psy9631 70 H 70 (90)
Q Consensus 70 ~ 70 (90)
.
T Consensus 380 ~ 380 (406)
T TIGR02034 380 P 380 (406)
T ss_pred c
Confidence 4
Homologous to this E.coli activation pathway are nodPQH gene products found among members of the Rhizobiaceae family. These gene products have been shown to exhibit ATP sulfurase and APS kinase activity, yet are involved in Nod factor sulfation, and sulfation of other macromolecules. With members of the Rhizobiaceae family, nodQ often appears as a fusion of cysN (large subunit of ATP sulfurase) and cysC (APS kinase).
