Elongation factor: Difference between revisions

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<StructureSection load='1efu' size='350' side='right' caption='Structure of EF-Tu (cyan and magenta) with EF-Ts (green and yellow) (PDB entry [[1efu]])' scene='51/517376/Cv/1'>
<StructureSection load='' size='350' side='right' caption='Structure of EF-Tu (cyan and magenta) with EF-Ts (green and yellow) (PDB entry [[1efu]])' scene='51/517376/Cv/1'>
__FORCETOC__
 
== Function ==


'''Elongation factors''' (EF) facilitate translational elongation during the formation of peptide bonds in the ribosome.<br />
'''Elongation factors''' (EF) facilitate translational elongation during the formation of peptide bonds in the ribosome.<br />
* '''EF-selB''' is selenocysteine-specific EF.<br />
* '''EF-selB''' is selenocysteine-specific EF. See [[SelB]]<br />
* '''EF-Tu or EF 1-α''' (elongation factor thermo unstable) is a prokaryotic EF.  EF-Tu contributes to translational accuracy.  It catalyzes the addition of aminoacyl tRNA<ref>PMID:20798060</ref>. <br />
* '''EF-Tu or EF 1-α''' (elongation factor thermo unstable) is a prokaryotic EF.  EF-Tu contributes to translational accuracy.  It catalyzes the addition of aminoacyl tRNA<ref>PMID:20798060</ref>. <br />
*'''EF-Ts or EF 1-β''' (elongation factor thermo stable) catalyzes the release of GDP from EF-Tu.<br />
*'''EF-Ts or EF 1-β''' (elongation factor thermo stable) catalyzes the release of GDP from EF-Tu.<br />
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*  '''EF-1 γ''' acts during the delivery of aminoacyl tRNA to the ribosome.<br />
*  '''EF-1 γ''' acts during the delivery of aminoacyl tRNA to the ribosome.<br />
* '''EF-2''' promotes the translocation of the nascent protein chain from the A site to the P site on the ribosome<ref>PMID:16246167</ref>.<br />
* '''EF-2''' promotes the translocation of the nascent protein chain from the A site to the P site on the ribosome<ref>PMID:16246167</ref>.<br />
* '''EF-3''' is a unique EF in fungi hence it provides an anti-fungal drug target.<br />
* '''EF-3''' is a unique EF in fungi hence it provides an anti-fungal drug target. See [[HEAT Repeat]]<br />
* '''EF Spt4, Spt5, Spt6''' are conserved among eukaryotes.  They modulate the chromatin structure.<br />
* '''EF Spt4, Spt5, Spt6''' are conserved among eukaryotes.  They modulate the chromatin structure.<br />
* '''EF-CA150''' is believed to play a role in coupling transcription and splicing.<br />
* '''EF-CA150''' is believed to play a role in coupling transcription and splicing.<br />
*  '''Elongin B and C complex''' is involved in the proteasomal degredation of target proteins.<br />
*  '''Elongin complex''' or '''SIII''' activates elongation by RNA polymerase II by suppressing transient pausing of the enzyme<ref>PMID:7660129</ref>.  The complex is composed of elongin A, B and C.  '''Elongin A''' (EloA) is the active component of the complex.  '''Elongin B and C''' (EloBC) are the regulatory subunits of it.  '''Von Hippel-Landau tumor suppressor protein''' (VHL) binds to EloBC and inhibits transcriptional elongation.<br />
For EF-3 see [[HEAT Repeat]]<br />
* '''Negative EF''' (NELF) are involved in regulating the pausing of RNA Pol II polymerase transcripton<ref>PMID:38401543</ref>.<br />
For EF-SelB see [[SelB]].


</StructureSection>
<scene name='51/517376/Cv/4'>Complex EF-Tu with EF-Ts is heterotetramer</scene>, or, more exactly <scene name='51/517376/Cv/5'>heterodimer of homodimers</scene> (PDB entry [[1efu]]).<ref>PMID:8596629</ref>  


==3D structures of elongation factor==
==3D structures of elongation factor==
[[Elongation factor 3D structures]]


Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
</StructureSection>
{{#tree:id=OrganizedByTopic|openlevels=0|
 
*EF-Tu
 
**[[1efm]], [[1efc]], [[1dg1]], [[2fx3]], [[1etu]] – EcEF – ''Escherichia coli''<BR />
**[[1qzd]] – EcEF – Cryo EM<BR />
**[[3u2q]] – EcEF + drug<BR />
**[[1mj1]] – EcEF + Phe-tRNA + S12 + S13 + L11 – Cryo EM<BR />
**[[3ep2]] - EcEF + tRNA + S12 + L11 + 16SRRNA + 23SRRNA – Cryo EM<BR />
**[[1ttt]], [[1ob5]] – TaEF + Phe-tRNA + GDPNP - ''Thermus aquaticus''<BR />
**[[1b23]] - TaEF + Cys-tRNA<BR />
**[[1ls2]] – yEF + Phe-tRNA – yeast – Cryo EM<BR />
**[[3agj]] – ApEF + plethora protein – ''Aeropyrum pernix''<br />
**[[4h9g]], [[4lbv]], [[4lbw]], [[4lby]], [[4lbz]], [[4lc0]] – TtEF – ''Thermus thermophilus''<br />
**[[4j0q]] – EF – ''Pseudomonas putida''<br />
 
*''EF-Tu complex with antibiotics''
 
**[[1ob2]] - yEF + Phe-tRNA + antibiotic<BR />
**[[4abr]] - TtEF + antibiotic in 30S ribosome<BR />
**[[1ha3]] - TtEF + antibiotic + GDP<BR />
**[[2c77]], [[2c78]] - TtEF + antibiotic + GTP analog<br />
**[[3fic]], [[3fic]] – TtEF + antibiotic in 70S ribosome – Cryo EM<BR />
**[[2bvn]] - EcEF + GDP<BR />NP + antibiotic<BR />
**[[1d8t]], [[2hcj]], [[2hdn]], [[3u6b]], [[3u6k]], [[4g5g]] – EcEF + antibiotic
 
*''EF-Tu complex with nucleotide''
 
**[[1efu]] – EcEF + GDP<BR />
**[[1exm]] – TtEF + GTP analog<br />
**[[1eft]] – TaEF + GNP – ''Thermus aquaticus''<BR />
**[[1tui]] – TaEF + GDP<BR />
**[[1d2e]] – bEF + GDP – bovine<BR />
**[[1jny]], [[1skq]] – SsEF + GDP – ''Sulfolobus solfataricus''<br />
**[[3wya]] – PhEF + GDP - ''Pyrococcus horikoshii''<br />
 
*''EF-Tu complex with protein''
 
**[[3vmf]] – ApEF + translation termination factor<br />
**[[3wxm]] – ApEF + protein pelota homolog<br />
**[[3wy9]] – PhEF + L12 <br />
**[[4p3y]] – EcEF + thiol:disulfide interchange protein <br />
 
*''EF-Tu with EF-Ts''
 
**[[1efu]], [[3agp]], [[3agq]] – EcEF + EcEF-Ts<BR />
**[[3avt]], [[3avu]] , [[3avv]], [[3avw]], [[3avx]], [[3avy]], [[3vnu]] , [[3vnv]], [[4fwt]] – EcEF + EcEF-Ts + RNA<br />
**[[3mmp]] – EcEF + EcEF-Ts + RNA replicase beta chain<br />
**[[4q7j]] – EcEF + EcEF-Ts + Q beta replicase + S1<br />
**[[1aip]] - TtEF + TtEF-Ts - ''Thermus thermophilus''<BR />
**[[1xb2]] – bEF + EF-Ts - bovine<BR />
**[[1f60]]  – yEF + EF-Ts C terminal<BR />
**[[1g7c]] - yEF + EF-Ts C terminal + GDPNP<BR />
**[[1ije]], [[1ijf]] - yEF + EF-Ts C terminal + GDP<BR />
**[[2b7b]] - yEF + EF-Ts C terminal (mutant) + GDP<BR />
**[[2b7c]] - yEF + EF-Ts C terminal (mutant)
 
*''EF-Tu in the ribosome''
 
**[[3eq3]], [[3eq4]] – EcEF in 80S ribosome – Cryo EM<BR />
**[[3izv]], [[3izw]], [[3fih]] -  EcEF in 30S ribosome – Cryo EM<BR />
**[[1zc8]], [[3dwu]] – TtEF in 70S ribosome – Cryo EM<BR />
**[[2wrn]], [[2wrq]], [[2xqd]], [[2y0u]], [[2y0w]], [[2y0y]], [[2y10]], [[2y12]], [[2y14]], [[2y16]], [[2y18]] - TtEF in 70S ribosome
 
*EF-SII
 
**[[1tfi]] – hEF – human – NMR<BR />
**[[3ndq]] - hEF domain II<BR />
**[[1enw]] – yEF domain II – NMR<BR />
**[[1eo0]] -  yEF domain I – NMR<BR />
**[[2xex]] – SaEF – ''Staphylococcus aureus''<BR />
**[[1pqv]], [[1y1v]] – yEF + RNA polymerase II<BR />
**[[1y1y]], [[3gtm]] – yEF + RNA polymerase II + RNA<BR />
**[[1wjt]] – mEF N terminal – mouse – NMR<BR />
**[[2m1h]] – EF PWWP domain – ''Trypanosoma brucei'' – NMR<br />
 
*EF-ELL2
 
**[[2e5n]] – hEF N2 domain - NMR<BR />
 
*EF-G
 
**[[1efg]], [[1elo]], [[1ktv]], [[1wdt]], [[2dy1]] – TtEF<BR />
**[[4m1k]], [[4myt]], [[4myu]] – TtEF (mutant)<br />
**[[1pn6]], [[3izp]] – TtEF – Cryo EM<BR />
**[[4b8f]], [[4b8h]] – TtEF in 70S ribosome <BR />
**[[4juw]], [[4kbt]], [[4kbv]], [[4kcy]], [[4kd0]], [[4kd8]], [[4kda]], [[4kdg]], [[4kdj]], [[4btc]] – TtEF in 30S ribosome <BR />
**[[4kiy]], [[4kj0]], [[4kj2]], [[4kj4]], [[4kj6]], [[4kj8]], [[4kja]], [[4kjc]] – EcEF in 30S ribosome <BR />
**[[3j5n]] – EcEF in 30S ribosome – Cryo-EM<BR />
**[[3j5x]] – EcEF in 30S ribosome + antibiotics – Cryo-EM<BR />
**[[1fnm]], [[2bm0]], [[2bm1]] – TtEF (mutant) <BR />
**[[2bcw]] – TtEF + L11 + L7/L12 <br />
**[[2xex]] – SaEF<BR />
**[[3zz0]], [[3zzt]], [[3zzu]] – SaEF (mutant) <BR />
**[[2bv3]] - TtEF (mutant) + GTP analog<br />
**[[2j7k]] - TtEF (mutant) + GDP analog<br />
**[[2om7]], [[2wri]], [[2wrk]] – TtEF in 70S ribosome – Cryo EM<BR />
**[[2xsy]], [[2xuy]] - TtEF in 70S ribosome<BR />
**[[1dar]], [[2efg]] – TtEF + GDP<BR />
**[[1jqm]], [[1jqs]] – EcEF + L11 – Cryo EM<BR />
**[[1zn0]], [[2rdo]], [[3j0e]], [[3j18]] – EcEF in 30S ribosome – Cryo-EM<BR />
**[[4fn5]] – PaEF - ''Pseudomonas aeruginosa''<br />
 
*EF-GreA/GreB
 
**[[2pn0]] – EF – ''Nitrosomonas europaea''<BR />
**[[2p4v]] – EcEF-GreB<br />
**[[1grj]] – EcEF-GreA<br />
 
*EF-NusA
 
**[[1wcl]], [[1wcn]] – EcEF C terminal – NMR<BR />
**[[2kwp]] - EcEF N terminal – NMR<BR />
**[[2jzb]] – EcEF + RNA polymerase subunit α - NMR<BR />
 
*EF-P
 
**[[1ueb]] – TtEF<BR />
**[[3huw]], [[3huy]] – TtEF in 70S ribosome<BR />
**[[3oyy]] – PaEF <BR />
**[[3tre]] – EF – ''Coxiella burnetii''<br />
**[[3a5z]] – EcEF + lysyl-tRNA synthetase<br />
**[[1yby]] – EF – ''Clostridium thermocellum''<br />
 
*EF-Ts
 
**[[1tfe]] – TtEF<BR />
**[[1b64]] – hEF guanine exchange factor domain – NMR<BR />
**[[2cp9]] – UBA domain – NMR<BR />
**[[1gh8]] – EF – ''Methanobacterium thermoautotrophicum'' – NMR<BR />
**[[2yy3]] – PhEF <BR />
**[[2uz8]] – hEF (mutant)
 
*EF-1 α-2
 
**[[4c0s]] – rEF  – rabbit<br />
 
*EF-1 δ-1
 
**[[2mvm]], [[2mvn]] – hEF CAR domain – NMR<br />
 
*EF-1G
 
**[[1nhy]] – yEF N terminal
**[[1pbu]] – hEF C terminal (mutant) - NMR<BR />
 
*EF-2
 
**[[1n0v]] – yEF<BR />
**[[1u2r]] – yEF + GDP<BR />
**[[1n0u]], [[2e1r]], [[2npf]] – yEF + antifungal drug<BR />
**[[1zm2]], [[1zm3]], [[1zm4]], [[1zm9]], [[3b78]], [[3b82]], [[3b8h]], [[2zit]] – yEF + exotoxin<BR />
**[[1s1h]] - hEF  in 40S ribosome – Cryo EM<BR />
**[[4cxg]], [[4cxh]] - rEF  in 40S ribosome – Cryo EM<BR />
**[[2p8w]], [[2p8x]], [[3dny]] - yEF in 80S ribosome – Cryo EM<BR />
**[[2p8y]], [[2p8z]] - yEF+ antifungal drug in 80S ribosome – Cryo EM<BR />
 
*EF-3
 
**[[2ix3]] – yEF<BR />
**[[2iwh]] – yEF + ADPNP<BR />
**[[2iw3]] – yEF + ADP<BR />
**[[2ix8]] – yEF in 80S ribosome – Cryo EM<BR />
 
*EF-4 (lepA)
 
**[[2ywh]], [[2ywe]], [[2ywf]], [[2ywg]] - AalepA  + nucleotide - ''Aquifex aeolicus''<BR />
**[[3cb4]] - EclepA  <BR />
**[[3deg]] - EclepA  in 70S ribosome + GMPPNP – Cryo EM<BR />
 
*EF-SelB
 
**[[1lva]] – MtEF C terminal – ''Moorella thermoacetica''<BR />
**[[2v9v]] – MtEF winged helix domain<BR />
**[[1wsu]], [[2uwm]] – MtEF + RNA<BR />
**[[2ply]] – MtEF (mutant) + RNA<BR />
**[[1wb2]], [[4aca]] – MmEF – ''Methanococcus maripaludis''<BR />
**[[1wb3]], [[4acb]] – MmEF + GTP analog<br />
**[[4ac9]], [[1wb1]] – MmEF + GDP<BR />
**[[2pjp]] – EcEF + RNA
 
*EF-Spt5
 
**[[2do3]], [[2e6z]], [[2e70]] – hEF KOW motif – NMR<BR />
**[[2exu]] – yEF<BR />
**[[3h7h]] – hEF + hEF-Spt4
 
*EF-Spt6
 
**[[3gxw]], [[3gxx]], [[3pjp]] – EF SH2 domain – ''Candida glabrata''<BR />
**[[3psf]], [[3psi]] – yEF core domain<BR />
**[[3psj]], [[3psk]] – yEF SH2 domain<BR />
**[[2l3t]] - yEF SH2 domain]] - NMR<BR />
**[[3oak]] – yEF + transcription factor IWS1
 
*EF-CA150
 
**[[2dod]], [[2doe]], [[2dof]], [[2e71]], [[2kiq]], [[2kis]] – hEF FF domain – NMR<BR />
**[[3hfh]] – hEF FF domain<BR />
**[[2ysi]]– mEF WW domain - NMR<BR />
 
*Elongin BC complex


**[[1lqb]], [[1lm8]] – hEloBC + von-Hippel Lindau disease tumor suppressor + hypoxia inducible factor 1 α<br />
**[[3zrc]], [[3ztc]], [[3ztd]], [[3zun]] - hEloBC + von-Hippel Lindau disease tumor suppressor + inhibitor<br />
**[[3zrf]] - hEloBC + von-Hippel Lindau disease tumor suppressor<br />
**[[2c9w]], [[2izv]], [[2jz3]] – hEloBC + suppressor of cytokine signaling<br />
**[[3dcg]] – hEloBC + virion infectivity factor<br />
**[[2xai]] - hEloBC + ankyrin rep<br />
**[[1vcb]] – hEloBC + VHL<br />
**[[2fnj]] - mEloBC + GUSTAVUS
}}
== References ==
== References ==
<references/>
<references/>


[[Category:Topic Page]]
[[Category:Topic Page]]
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