Aminoacyl tRNA Synthetase: Difference between revisions

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<StructureSection load='1f7v' size='350' side='right' scene='' caption='Arginine tRNA synthetase complex with Arg-tRNA [[1f7v]]'>
<StructureSection load='' size='350' side='right' scene='44/444597/Cv/2' caption='Arginine tRNA synthetase complex with Arg-tRNA [[1f7v]]'>


'''Aminoacyl tRNA synthetase''' (aaRS) catalyzes the esterification of a specific amino acid to its cognate tRNA to form an aminoacyl-tRNA.  The amino acid is transferred by the ribosome from the aminoacylated-tRNA onto a growing polypeptide chain.  Class I of aaRS is a monomer or dimer, it has 2 highly conserved sequence motifs and it aminoacylates at the 2’-OH of an adenosine nucleotide. Class II of aaRS is a dimer or tetramer, it has 3 highly conserved sequence motifs and it aminoacylates at the 3’-OH of an adenosine nucleotide.  CP1 domain of RS edits a mischarged aa-tRNA.  Some of the crystal structures are complexes of the RS with their reactant analog: amino acid-sulfamoyl adenine (aa-SA).<ref>PMID:8422978</ref> For '''pyrrolysyl-RS''' details see [[Pyrrolysyl-tRNA synthetase]].
'''Aminoacyl tRNA synthetase''' (aaRS) or '''aminoacyl tRNA ligase''' catalyzes the esterification of a specific amino acid to its cognate tRNA to form an aminoacyl-tRNA.  The amino acid is transferred by the ribosome from the aminoacylated-tRNA onto a growing polypeptide chain.  Class I of aaRS is a monomer or dimer, it has 2 highly conserved sequence motifs and it aminoacylates at the 2’-OH of an adenosine nucleotide. Class II of aaRS is a dimer or tetramer, it has 3 highly conserved sequence motifs and it aminoacylates at the 3’-OH of an adenosine nucleotide.  CP1 domain of RS edits a mischarged aa-tRNA.  Some of the crystal structures are complexes of the RS with their reactant analog: amino acid-sulfamoyl adenine (aa-SA).<ref>PMID:8422978</ref>.
*'''Bifunctional tRNA synthetase''' can lad tRNA molecules with either Glu or Pro <ref>PMID:34537243</ref>.
*'''Phosphoserine tRNA synthetase''' is used by ''Methanocaldococcus jannaschii'' to produce Cys <ref>PMID:18425141</ref>.
*For '''leucine-RS''' details see [[Leucyl-tRNA Synthetase]].
*For '''pyrrolysyl-RS''' of '''pyrrolysine-tRNA ligase''' details see [[Pyrrolysyl-tRNA synthetase]].
*For '''threonyl-RS''' see [[User:Khadar_Abdi/Sandbox1]]
 
See also [[TRNA synthetases (Hebrew)]].


</StructureSection>
== 3D Structures of Aminoacyl tRNA synthetase ==
== 3D Structures of Aminoacyl tRNA synthetase ==
[[Aminoacyl tRNA synthetase 3D structures]]


Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
One very interesting question in biology is how does an aminoacyl-tRNA synthetase recognize a particular tRNA and charge it with the correct amino acid?  This is a challenging problem, since all tRNAs have the same general structure.  Interestingly, different tRNA synthetases accomplish this goal in different ways.


{{#tree:id=OrganizedByTopic|openlevels=0|
The <scene name='44/444597/Protein_surface_interaction/2'>glutaminyl-tRNA synthetase</scene> (GlnRS) interacts with both <scene name='44/444597/Acceptor_and_anticodon_interac/1'>the anticodon loop and the acceptor stem</scene>.  Genetic and biochemical data indicate that GlnRS interacts with all three bases of the <scene name='44/444597/Anticodon_loop/3'>anticodon loop</scene>, which are unstacked and splay outward so they can bind in separate recognition pockets of GlnRS.    The 3' end of tRNAgln plunges deeply into a protein pocket that also binds the enzyme's <scene name='44/444597/Atp_binding_site/1'>ATP</scene> and glutamine substrates.


*'''Class I aaRS'''
One interesting question is how tRNA synthetases are able to discern that the correct amino acid is loaded.  The structure for aspartate is very similar to glutamine, differing only by an amino group and one CH2 group.  However, the aminoacyl tRNA synthetases interact with the tRNA in completely different fashions.  Asp-tRNA synthetase acts as a <scene name='44/444597/Asp_trna_synthetase/1'>dimer</scene>, and interacts with the opposite face of the tRNA, the <scene name='44/444597/Major_groove_binding/1'>major groove</scene> side.  The anticodon arm of tRNA Asp is bent by as much as 20 A toward the inside of the L relative to that in the X-ray structure of uncomplexed tRNA Asp, and its anticodon bases are unstacked. The hinge point for the bend is a <scene name='44/444597/U40_g30_h_bond/1'>G30 • U40</scene> base pair in the anticodon stem (nearly all other species of tRNA contain a Watson-Crick base pair at that point)


*'''Arg-RS'''
</StructureSection>
 
**[[1bs2]] – yArgRS<br />
**[[3gdz]] – ArgRS  residues 1-106 – ''Klebsiella pneumoniae''<br />
**[[1iq0]] – TtArgRS  - ''Thermus thermophilus''
 
*''Arg-RS + tRNA''
 
**[[2zuf]] - PhArgRS  + Arg-tRNA - ''Pyrococcus horikoshii''<br />
**[[1f7v]] - yArgRS  + Arg-tRNA
 
*''Arg-RS ternary complex''
 
**[[1f7u]] – yArgRS  + Arg-tRNA + Arg<br />
**[[2zue]] – PhArgRS  + Arg-tRNA + ATP analog
 
*'''Cys-RS'''
 
**[[1li5]] - EcCysRS - ''Escherichia coli''<br />
**[[1li7]] - EcCysRS + Cys<br />
**[[1u0b]] – EcCysRS + Cys-tRNA
 
*'''Gln-RS'''
 
**[[1nyl]]– EcGlnRS<br />
**[[2gls]], [[1lgr]] – StGlnRS – ''Salmonella typhimurium''<br />
**[[2lgs]] – StGlnRS + Glu<br />
**[[1qrt]], [[1qru]], [[1qrs]] - EcGlnRS (mutant) + Gln-tRNA<br />
**[[1gtr]], [[1gts]], [[1gsg]] - EcGlnRS + Gln-tRNA<br />
**[[1qtq]] - EcGlnRS + Gln-tRNA + Gln analog
 
*''Gln-RS ternary complex''
 
**[[1euq]], [[ 1euy]] – EcGlnRS + Gln-tRNA + Gln-SA<br />
**[[1exd]] - EcGlnRS + Gln-tRNA (mutant) + AMP
 
*'''Glu-RS'''
 
**[[1gln]] – TtGluRS<br />
**[[2o5r]] - TmGluRS<br />
**[[3aii]] – GluRS – ''Methanothermobacter thermautotrophicus''<br />
**[[2ja2]] – MtGluRS – ''Mycobacterium tuberculosis''<br />
**[[2zlz]] – EcGluRS<br />
**[[2hz7]] – DrGluRS – ''Deinococcus radiodurans''<br />
**[[2hra]] – yGluRS N-terminal
*''Glu-RS + small substrates or analogs''
 
**[[3afh]] - TmGluRS + Glu-AMP analog<br />
**[[2rd2]], [[ 2re8]] – EcGluRS (mutant) + Glu-SA<br />
**[[2cuz]] – TtGluRS + Glu<br />
**[[1j09]] - TtGluRS + Glu + ATP<br />
**[[1n75]] - TtGluRS + ATP<br />
**[[2fco]] - GluRS residues 2-485 + Glu – ''Synechococcus elongatus''
 
*''Glu-RS + tRNA''
 
**[[1zjw]] – EcGluRS + Glu-tRNA
 
*''Glu-RS ternary complex''
 
**[[3akz]], [[ 3al0]] – TmGluRS + tRNA + Glu-AMP analog – ''Thermotoga maritima''<br />
**[[1o0b]], [[ 1o0c]] - EcGluRS + Glu-tRNA + Glu + AMP<br />[[2cv0]], [[ 1n77]] - TtGluRS + Glu + Glu-tRNA<br />
**[[1n78]] - TtGluRS + Glu-ol + Glu-tRNA<br />
**[[2cv1]] - TtGluRS + Glu-ol + ATP + Glu-tRNA<br />
**[[2cv2]] - TtGluRS + Glu-SA + Glu-tRNA<br />
**[[2hrk]], [[ 2hsm]] - yGluRS N-terminal + GU4 nucleic-binding protein 1
 
*'''Ile-RS'''
 
**[[1ile]] - TtIleRS<br />
**[[1wny]], [[ 1udz]] – TtIleRS editing domain
 
*''Ile-RS + small substrates or analogs''<br />
 
**[[1ue0]] - TtIleRS editing domain + Val<br />
**[[1wnz]] - TtIleS editing domain + Val-adenylate<br />
**[[1wk8]] - TtIleRS editing domain + Val-SA<br />
**[[1jzq]] – TtIleS + Ile-adenylate analog<br />
**[[1jzs]] – TtIleS + antibiotic
 
*''Ile-RS ternary complex''<br />
 
**[[1ffy]], [[ 1qu2]], [[ 1qu3]] - SaIleRS + Ile-tRNA + antibiotic - ''Staphylococcus aureus''
 
*'''Leu-RS'''
 
**[[3o0a]] – AaLeuRS hydrolytic domain – ''Aquifex aeolicus''<br />[[2wfd]] – hLeuRS editing domain – human<br />
**[[2wfe]] - CaLeuRS editing domain – ''Candida albicans''<br />
**[[2ajg]] - EcLeuRS editing domain<br />
**[[1wkb]] – PhLeuRS residues 1-810
 
*''Leu-RS + small substrates or analogs''<br />
 
**[[2wfg]] - CaLeuRS editing domain + benzoxaborole-AMP<br />
**[[2v0c]] – TtLeuRS + Leu-SA + benzoxaborole-AMP<br />
**[[1h3n]] - TtLeuRS + Leu-SA<br />
**[[1obc]], [[1obh]] – TtLeuRS + substrate analog<br />
**[[2ajh]], [[2aji]] - EcLeuRS editing domain + aa
 
*''Leu-RS + tRNA''<br />
 
**[[1wz2]] – PhLeuRS Leu-tRNA
 
*''Leu-RS ternary complex''<br />
 
**[[2v0g]] - TtLeuRS + Leu-tRNA + benzoxaborole-AMP<br />
**[[2bte]], [[ 2byt]] - TtLeuRS + Leu-tRNA + Leu
 
*'''Lys-RS'''
 
**[[1irx]] – PhLysRS<br />
**[[1bbw]] – EcLysRS<br />
**[[1krs]], [[ 1krt]] – EcLysRS anticodon-binding domain – NMR<br />[[3dsq]] – DhLysRS – ''Desulfitobacterium hafniense''<br />
**[[2e3c]] - MmLysRS catalytic domain - ''Methanosarcina mazei''<br />
**[[3bju]] – hLysRS residues 70-579
 
*''Lys-RS + small substrates or analogs''<br />
 
**[[3a74]] – GsLysRS + diadenosine tetraphosphate – ''Geobacillus stearothermophilus''<br />
**[[3e9h]], [[3e9i]] – BsLysRS + Lys-SA - ''Bacillus stearothermophilus''<br />
**[[2zin]] – MmLysRS catalytic domain + Boc-Lys + ATP analog<br />
**[[2zio]] - MmLysRS catalytic domain + Aloc-Lys-AMP + PNP<br />
**[[2zcd]] - MmLysRS catalytic domain + AMPPNP<br />
**[[2zce]] - MmLysRS catalytic domain + pyrro-Lys + ATP analog<br />
**[[2zim]] - MmLysRS residues 185-454+ pyrro-Lys-adenylate<br />
**[[2q7e]] - MmLysRS C-terminal + ATP analog<br />
**[[2q7g]] - MmLysRS C-terminal+ pyrro-Lys analog+ ATP <br />
**[[1bbu]], [[1e10]], [[1lyl]] – EcLysRS + Lys<br />
**[[1e1t]] - EcLysRS + Lys-adenylate<br />
**[[1e22]] - EcLysRS + Lys + AMPPCP<br />
**[[1e24]] - EcLysRS + Lys + ATP
 
*''Lys-RS + tRNA''<br />
 
**[[2zni]], [[2znj]] – DhLysRS + tRNA
 
*'''Met-RS'''
 
**[[1a8h]] – TtMetRS<br />
**[[1med]], [[1mea]] – EcMetRS Zinc-binding domain - NMR<br />
**[[1qqt]] - EcMetRS residues 2-552<br />
**[[2x1l]] - MsMetRS residues 2-515 – ''Mycobacterium smegmatis''<br />
**[[3h97]] – EcMetRS residues 2-548 (mutant) <br />
**[[3h9c]] - EcMetRS residues 2-548<br />
**[[2d54]], [[2d5b]] – TtMetRS (mutant) <br />
**[[1woy]] – TtMetRS residues 1-500 (mutant) <br />
**[[2djv]] – hMetRS WHEP-TRS domain – NMR<br />
**[[1pyb]] – AaMetRS β subunit<br />
**[[1rqg]] – PaMetRS – ''Pyrococcus abyssi''<br />
**[[1mkh]] – PaMetRS C-terminal
 
*''Met-RS + small substrates or analogs''<br />
 
**[[3kfl]] – LmMetRS residues 206-747+ Met-adenylate - ''Leishmania major''<br />
**[[2x1m]] - MsMetRS residues 2-515 + Met<br />
**[[1p7p]], [[1pfu]], [[1pfv]], [[1pfw]] - EcMetRS residues 2-548 + Met<br />
**[[1pfy]] - EcMetRS residues 1-551 + Met-SA<br />
**[[1f4l]] - EcMetRS residues 1-551 + Met<br />
**[[1pg0]] - EcMetRS residues 1-551 + Met-adenylate<br />
**[[1pg2]] - EcMetRS residues 1-551 + Met + adenine<br />
**[[3h99]] - EcMetRS residues 2-548 (mutant) + Met<br />
**[[3h9b]] - EcMetRS residues 2-548 (mutant) + azidonorleucine<br />
**[[4dlp]] - MetRS + SMet – ''Brucella melitensis''
 
*''Met-RS + tRNA''<br />
 
**[[2csx]] – AaMetRS + Met-tRNA
 
*''Met-RS + tRNA''<br />
 
**[[2ct8]] - AaMetRS + Met-tRNA + Met-SA<br />
**[[2dxi]] – TtMetRS + tRNA + ATP + Glu-ol
 
*''Met-RS coplex''<br />
 
**[[4bl7]], [[4bvx]], [[4bvy]] - hMetRS N-terminal + elongation factor P18<br />
**[[2hsn]] - yMetRS N-terminal + GU4 nucleic-binding protein 1 N-terminal
 
*'''Trp-RS'''
 
**[[1d2r]] - GsTrpRS<br />
**[[3prh]] – TrpRS (mutant) – ''Bacillus subtilis''<br />
**[[3n9i]] – TrpRS – ''Yarsinia pestis''<br />
**[[3m5w]] – CjTrpRS – ''Campylobacter jejuni''<br />
**[[3a04]] – ApTrpRS – ''Aeropyrum pernix''<br />
**[[3hzr]] – EhTrpRS – ''Entamoeba histolytica'' <br />
**[[3i05]] – TbTrpRS residues 3-389 – ''Trypanosoma brucei''<br />
**[[3hv0]] – TRrpS residues 206-593 – ''Cryptosporidium parvum''<br />
**[[3foc]] – GlTrpRS – ''Giardia lamblia''<br />
**[[1o5t]] – hTrpRS catalytic fragment<br />
**[[1ulh]] – hTrpRS residues 35-424<br />
**[[2el7]] – TtTrpRS<br />
**[[2ip1]], [[3kt0]] – yTrpRS – yeast<br />
**[[2yy5]] – TrpRS – ''Mycoplasma pneumoniae''<br />
**[[2g36]] – TmTrpRS<br />
**[[1bks]] – StTrpRS + pyridoxal phosphate
 
*''Trp-RS + small substrates or analogs''<br />
 
**[[3a05]] – ApTrpRS + Trp<br />
**[[3kt3]] – yTrpRS + Trp-adenylate<br />
**[[3kt6]], [[3kt8]] – yTrpRS + Trp<br />
**[[3jxe]] – PhTrpRS + Trp-adenylate<br />
**[[3fhj]], [[3fio]] – BsTrpRS + Trp + AMP + Pi<br />
**[[2quh]] – hTrpRS + Trp<br />
**[[2qui]] - hTrpRS + Trp-amide + ATP<br />
**[[2quj]] - hTrpRS + Trp-adenylate<br />
**[[2quk]] – hTrpRS + ATP<br />
**[[2ov4]] – GsTrpRS + adenosine tetraphosphate<br />
**[[1i6k]], [[1i6l]], [[1i6m]] – GsTrpRS + Trp-adenylate<br />
**[[1yid]], [[2a4m]] – DrTrpRS + ATP<br />
**[[1yi8]], [[1yia]] – DrTrpRS + Trp<br />
**[[1mau]] – GsTrpRS + Trp + ATP<br />
**[[1maw]], [[ 1m83]] - GsTrpRS + ATP<br />
**[[1mb2]] - GsTrpRS + Trp <br />
**[[3tze]] - TrpRS + Trp - ''Encephalitozoon cuniculi''<br />
**[[3tzl]] - CjTrpRS + Trp + ADP<br />
**[[3sz3]] - TrpRS + Trp - ''Vibrio cholerae''<br />
 
*''Trp-RS + tRNA''<br />
 
**[[2ake]], [[2dr2]] - hTrpRS + Trp-tRNA
 
*'''Tyr-RS'''
 
**[[1tya]], [[ 1tyb]], [[ 1tyc]], [[ 1tyd]], [[ 2ts1]] – GsTyrRS<br />
**[[3qe4]], [[3d6u]], [[3d6v]], [[2pxh]], [[2hgz]], [[1u7d]] – MjTyrRS – ''Methanocaldococcus jannaschii''<br />
**[[1u7x]], [[4hjr]], [[4hk4]]- MjTyrRS (mutant) <br />
**[[2jan]] – MtTyrRS<br />
**[[1y42]] - NcTyrRS  – ''Neurospora crassa''<br />
**[[2cya]] – ApTyrRS<br />
**[[1n3l]] - hTyrRS residues 1-364<br />
**[[1r6t]], [[1r6u]] – yTyrRS (mutant) <br />
**[[1jh3]] – GsTyrRS C-terminal – NMR<br />
 
*''Tyr-RS + small substrates or analogs''<br />
 
**[[3ts1]] – GsTyrRS + Tyr-adenylate intermediate<br />
**[[4ts1]] – GsTyrRS + Tyr<br />
**[[3p0h]], [[3p0i]], [[3p0j]] – LmTyrRS + inhibitor<br />
**[[3n2y]] – MjTyrRS + tetrazolyl phenylalanine<br />
**[[2zp1]] – MjTyrRS (mutant) + Tyr<br />
**[[1zh0]] - MjTyrRS (mutant) + naphthyl-Ala<br />
**[[1zh6]] - MjTyrRS (mutant) + acetyl-Phe<br />
**[[2ag6]] - MjTyrRS (mutant) + bromo-Phe<br />
**[[4hjx]] - MjTyrRS (mutant) + di-fluoro-Tyr<br />
**[[2yxn]] – EcTyrRS residues 1-322 + azido-Tyr<br />
**[[1vbm]] – EcTyrRS + Tyr-SA<br />
**[[1vbn]] – EcTyrRS (mutant) + Tyr-SA<br />
**[[1wq3]], [[1wq4]] - EcTyrRS (mutant) + Tyr<br />
**[[1x8x]] – EcTyrRS + Tyr<br />
**[[2pid]] – hTyrRS residues 28-375 + Tyr-SA<br />
**[[2j5b]] – TyrRS residues 2-346 + Tyr-ol – ''Acanthamoeba polyphaga'' minivirus<br />
**[[2dlc]] – yTyrRS + tRNA + Tyr-SA<br />
**[[2cyb]] – AfTyrRS + Tyr - ''Archaeoglobus fulgidus''<br />
**[[2cyc]] – PhTyrRS + Tyr<br />
**[[1q11]] – hTyrRS residues 1-364 + Tyr-ol<br />
**[[1h3e]] - TtTyrRS + Tyr-tRNA + Tyr-ol + ATP<br />
**[[1h3f]] - TtTyrRS + Tyr-ol<br />
**[[1jh3]] – GsTyrRS C-terminal – NMR<br />
**[[1jii]], [[ 1jij]], [[1jil]], [[1jik]] – SaTyrRS + inhibitor
 
*''Tyr-RS + tRNA''<br />
 
**[[1j1u]] – MjTyrRS + Tyr-tRNA
 
**[[2rkj]] – NcTyrRS + RNA
 
*'''Val-RS'''
 
**[[1iyw]] - TtValRS<br />
**[[1wk9]], [[ 1wka]] – TtValRS CP1 domain
 
*''Val-RS ternary complex''<br />
 
**[[1ivs]] – TtValRS + Val-SA + Val-tRNA<br />
**[[1gax]] - TtValRS + Val-adenylate analog + Val-tRNA
 
*'''Class II aaRS'''
 
*'''Ala-RS'''
 
**[[3g98]] – AaAlaRS residues 758-867<br />
**[[1riq]] - AaAlaRS catalytic fragment<br />
**[[2zze]], [[ 2zzf]], [[ 1wnu]], [[ 1wxo]], [[ 1v4p]] – PhAlaRS<br />
**[[2zvf]] – AfAlaRS C-terminal
 
*''Ala-RS + small substrates or analogs''<br />
 
**[[3hxu]], [[3hxv]], [[3hxw]] – EcAlaRS catalytic fragment + aa-adenylate <br />
**[[3hxz]], [[3hy0]], [[3hy1]] - EcAlaRS catalytic fragment (mutant) + aa-adenylate<br />
**[[3hxx]] - EcAlaRS catalytic fragment + AMPPCP<br />
**[[3hxy]] - EcAlaRS catalytic fragment + AMPPCP + Ala-AMP + PCP<br />
**[[3htz]] - AaAlaRS residues 2-454 + Ser<br />
**[[1yfr]] – AaAlaRS + ATP<br />
**[[1yfs]]  – AaAlaRS + Ala<br />
**[[1yft]], [[1ygb]] - AaAlaRS catalytic fragment + aa<br />
**[[2zzg]] - PhAlaRS + Ala-SA<br /
**[[2ztg]] – AfAlaRS + Ala-SA<br />
 
*'''Asp-RS'''
 
**[[3nen]], [[1b8a]] – TkAspRS - ''Thermococcus kodakarensis''<br />
**[[3i7f]] – EhAspRS<br />
**[[1wyd]] – AspRS – ''Sulfolobus tokodaii''<br />
**[[1eov]] - yAspRS<br />
**[[1n9w]], [[1l0w]], [[1g51]] – TtAspRS<br />
**[[1eqr]] – EcAspRS
 
*''Asp-RS + small substrates or analogs''<br />
 
**[[3nel]] – TkAspRS + Asp <br />
**[[3nem]] - TkAspRS + Asp-adenylate
 
*''Asp-RS + tRNA''<br />
 
**[[3kfu]], [[1efw]] – TtAspRS + tRNA <br />
**[[1asy]], [[1asz]] – yAspRS + Asp-tRNA
 
*''Asp-RS ternary complex''<br />
 
**[[1il2]], [[1c0a]] – EcAspRS + Asp-tRNA + Asp-adenylate
 
*'''Asn-RS'''
 
**[[1x56]] - PhAsnRS <br />
**[[2kqr]] – BmAsnRS N-terminal – NMR – ''Brugia malayi''
 
*''Asn-RS + small substrates or analogs''<br />
 
**[[2xti]] – BmAsnRS catalytic fragment + Asn-adenine analog<br />
**[[2xgt]] - BmAsnRS catalytic fragment + Asn-SA<br />
**[[1x54]] – PhAsnRS + Asn-adenylate<br />
**[[1x55]] - PhAsnRS + Asn-SA<br />
**[[11as]] – EcAsnRS + Asn<br />
**[[12as]] - EcAsnRS + Asn + AMP
 
*'''Gly-RS'''
 
**[[1ati]] – TtGlyRS<br />
**[[2q5h]] – hGlyRS residues 55-739<br />
**[[2q5i]] - hGlyRS residues 55-739 (mutant) <br />
**[[2pme]] – hGlyRS<br />
**[[2pmf]] – hGlyRS (mutant) <br />
**[[1j5w]] – TmGlyRS α chain
 
*''Gly-RS + small substrates or analogs''<br />
 
**[[2zt5]], [[ 2zxf]] – hGlyRS residues 55-739 + bis-adenosine tetraphosphate<br />
**[[2zt6]] - hGlyRS residues 55-739 + AMPCPP<br />
**[[2zt7]] - hGlyRS residues 55-739 + Gly + ATP<br />
**[[2zt8]] - hGlyRS residues 55-739 + Gly-AMP analog<br />
**[[1b76]] – TtGlyRS + ATP<br />
**[[1ggm]] – TtGlyRS + Gly-adenylate
 
*'''His-RS'''
 
**[[3net]] – HisRS – Nostoc<br />
**[[1h4v]] – TtHisRS<br />
**[[1qe0]] – SaHisRS<br />
**[[3hri]] – TbHisRS<br />
**[[1x59]] – hHisRS WHEP-TRS domain - NMR
 
*''His-RS + small substrates or analogs''<br />
 
**[[3lc0]] – HisRS residues 45-478 + His – ''Trypanosoma cruzi''<br />
**[[1adj]] – TtHisRS + His <br />
**[[3hrk]] - TbHisRS + His-adenylate<br />
**[[2el9]] - EcHisRS + His-SA<br />
**[[1kmm]], [[1ady]] - EcHisRS + His-adenylate<br />
**[[1kmn]] - EcHisRS + His-ol + ATP
 
*'''Phe-RS'''
 
**[[1pys]] – TtPheRS<br />
**[[3l4g]], [[ 3cmq]] – hPheRS<br />
**[[2cxi]] – PhPheRS β chain N-terminal<br />[[3ica]] – PheRS β chain – ''Porphyromonas gingivalis''
*''Phe-RS + small substrates or analogs''<br />
 
**[[3pco]] – EcPheRS + phenylalanine+ AMP<br />
**[[3hfz]], [[2amc]] – TtPheRS α+β chains + Tyr<br />
**[[2akw]], [[1b70]] - TtPheRS α+β chains + Phe<br />
**[[1jjc]], [[1b7y]] - TtPheRS α+β chains + Phe-adenylate<br />
**[[2aly]] - TtPheRS α+β chains + Phe-SA<br />
**[[2rhq]], [[2rhs]] – PheRS α+β chains (mutant) + inhibitor – ''Staphylococcus haemolyticus''
 
*''Phe-RS + tRNA''<br />
 
**[[1eiy]] - TtPheRS α+β chains + Phe-tRNA
 
*''Phe-RS ternary complex''
 
**[[2iy5]] - TtPheRS α+β chains + Phe-ol + Phe-tRNA
 
*'''Pro-RS'''
 
**[[1hc7]] – TtProRS<br />
**[[2i4l]] – RpProRS – ''Rhodopseudomonas palustris''<br />
**[[1nj2]] - MtProRS – ''Methanothermobacter thermautotrophicus''<br />
**[[1nj8]] – MjProRS
 
*''Pro-RS + small substrates or analogs''<br />
 
**[[3ial]] – GlProRS residues 34-542 + Pro-adenylate<br />
**[[2i4m]], [[2i4n]] – RpProRS + aa-SA<br />
**[[2i4o]] – RpProRS + ATP<br />
**[[2j3l]] – EfProRS + Pro-SA – ''Enterococcus faecalis''<br />
**[[2j3m]] – EfProRS + Pro-ol + ATP<br />
**[[1nj1]], [[1nj5]], [[1nj6]] – MtProRS + aa-SA<br />
**[[1h4t]] - TtProRS + Pro
 
*''Pro-RS ternary complex''<br />
 
**[[1h4q]] - TtProRS + Pro-tRNA + Pro-ol<br />
**[[1h4s]] - TtProRS + Pro-tRNA + Pro-SA<br />
 
*'''Pyrrolysyl-RS'''
 
**[[2e3c]] - MmPylRS catalytic domain <br />
**[[3vqw]], [[3vqx]], [[4cs2]] - MmPylRS catalytic domain (mutant)<br />
**[[3dsq]] – DhPylRS <br />
 
*''Pyrrolysyl-RS binary complex''
 
**[[3qtc]] – MmPylRS catalytic domain (mutant) + AMP-ATP analog<br />
**[[2q7e]] - MmPylRS catalytic domain + ATP analog<br />
**[[2zcd]] - MmPylRS catalytic domain + AMP-ATP analog<br />
**[[3vqv]] - MmPylRS catalytic domain + AMPPNP <br />
**[[2zni]] – DhPylRS + tRNA <br />
**[[4ch3]], [[4ch4]], [[4ch5]], [[4ch6]] - MmPylRS catalytic domain + adenylated lysine derivative<br />
**[[4cs3]] - MmPylRS catalytic domain (mutant) + adenylated lysine derivative<br />
 
*''Pyrrolysyl-RS ternary complex''
 
**[[2zce]] - MmPylRS catalytic domain + pyrrolysine + ATP analog<br />
**[[2q7g]] - MmPylRS catalytic domain + pyrrolysine analog + ATP<br />
**[[2zim]], [[2q7h]] - MmPylRS catalytic domain + adenylated pyrrolysine + pyrophosphate<br />
**[[2zio]] - MmPylRS catalytic domain + AlocLys-AMP + ATP analog<br />
**[[3vqy]] - MmPylRS catalytic domain + butoxycarbonyl lysine + AMPPNP <br />
**[[4q6g]] - MmPylRS catalytic domain + acetyl lysine + ADPNP <br />
**[[4tqd]] - MmPylRS catalytic domain + iodo-Phe + ATP <br />
**[[4tqf]] - MmPylRS catalytic domain + bromothienylo-Ala + ATP <br />
**[[2zin]] - MmPylRS catalytic domain + butoxycarbonyl lysine + ATP analog <br />
 
*'''Ser-RS'''
 
**[[3lsq]] – TbSerRS<br />
**[[1sry]] - TtSerRS<br />
**[[3err]] – TtSerRS/dynein heavy chain<br />
**[[2zr3]] – PhSerRS<br />
**[[2dq3]] – AaSerRS<br />
**[[2du7]] – MjSerRS<br />
**[[2odr]] – SerRS – ''Methanococcus maripaludis''<br />
**[[2cim]] – MbSerRS – ''Methanosarcina barkeri''<br />
**[[1wle]] – SerRS – bovine
 
*''Ser-RS + small substrates or analogs''<br />
 
**[[2zr2]] – PhSerRS + ATP<br />
**[[2cj9]] – MbSerRS + Ser-SA<br />
**[[2cjb]] – MbSerRS + Ser<br />
**[[2cja]] – MbSerRS + ATP<br />
**[[1ses]], [[1set]] – TtSerRS + Ser-adenylate analog<br />
**[[3lss]] – TbSerRS + ATP
 
*''Ser-RS + tRNA''<br />
 
**[[1ser]] – TtSerRS + Ser-tRNA<br />
**[[2du4]] - AfSerRS + Cys-tRNA
 
*''Ser-RS ternary complex''<br />
 
**[[2du3]] – AfSerRS + Cys-tRNA + phosphoserine<br />
**[[2du5]], [[2du6]] - AfSerRS (mutant) + Cys-tRNA + phosphoserine
 
*'''Thr-RS'''
 
**[[1y2q]] - PaThrRS editing domain<br />
**[[1wwt]] – hThrRS TGS domain – NMR<br />
**[[1tje]] - EcThrRS editing domain
 
*''Thr-RS + small substrates or analogs''<br />
 
**[[3pd2]], [[3pd3]], [[3pd4]], [[3pd5]] – PaThrRS editing domain + aa-aminoadenosine<br />
**[[2hkz]] – PaThrRS editing domain + Ser<br />
**[[2hl0]], [[2hl1]] - PaThrRS editing domain + Ser-adenylate<br />
**[[2hl2]] - PaThrRS editing domain + Ser-SA<br />
**[[1tke]] - EcThrRS editing domain + Ser<br />
**[[1tkg]] - EcThrRS editing domain + Ser-SA<br />
**[[1tky]] - EcThrRS editing domain + Ser-adenylate<br />
**[[1fyf]], [[1evl]] - EcThrRS catalytic and anticodon-binding domains + aa-SA<br />
**[[1evk]] - EcThrRS catalytic and anticodon-binding domains + Thr<br />
**[[1nyq]] – SaThrRS + Thr-SA<br />
**[[1nyr]] – SaThrRS + ATP
 
*''Thr-RS + tRNA''<br />
 
**[[1qf6]] – EcThrRS + Thr-tRNA<br />
**[[1kog]] – EcThrRS catalytic and anticodon-binding domains + mRNA
 
*Multifunctional RS


**[[1fyj]] – hRS - NMR
}}
== References ==
== References ==
<references/>
<references/>
[[Category:Topic Page]]
[[Category:Topic Page]]

Latest revision as of 12:31, 23 May 2024


Aminoacyl tRNA synthetase (aaRS) or aminoacyl tRNA ligase catalyzes the esterification of a specific amino acid to its cognate tRNA to form an aminoacyl-tRNA. The amino acid is transferred by the ribosome from the aminoacylated-tRNA onto a growing polypeptide chain. Class I of aaRS is a monomer or dimer, it has 2 highly conserved sequence motifs and it aminoacylates at the 2’-OH of an adenosine nucleotide. Class II of aaRS is a dimer or tetramer, it has 3 highly conserved sequence motifs and it aminoacylates at the 3’-OH of an adenosine nucleotide. CP1 domain of RS edits a mischarged aa-tRNA. Some of the crystal structures are complexes of the RS with their reactant analog: amino acid-sulfamoyl adenine (aa-SA).[1].

See also TRNA synthetases (Hebrew).

3D Structures of Aminoacyl tRNA synthetase

Aminoacyl tRNA synthetase 3D structures

One very interesting question in biology is how does an aminoacyl-tRNA synthetase recognize a particular tRNA and charge it with the correct amino acid? This is a challenging problem, since all tRNAs have the same general structure. Interestingly, different tRNA synthetases accomplish this goal in different ways.

The (GlnRS) interacts with both . Genetic and biochemical data indicate that GlnRS interacts with all three bases of the , which are unstacked and splay outward so they can bind in separate recognition pockets of GlnRS. The 3' end of tRNAgln plunges deeply into a protein pocket that also binds the enzyme's and glutamine substrates.

One interesting question is how tRNA synthetases are able to discern that the correct amino acid is loaded. The structure for aspartate is very similar to glutamine, differing only by an amino group and one CH2 group. However, the aminoacyl tRNA synthetases interact with the tRNA in completely different fashions. Asp-tRNA synthetase acts as a , and interacts with the opposite face of the tRNA, the side. The anticodon arm of tRNA Asp is bent by as much as 20 A toward the inside of the L relative to that in the X-ray structure of uncomplexed tRNA Asp, and its anticodon bases are unstacked. The hinge point for the bend is a base pair in the anticodon stem (nearly all other species of tRNA contain a Watson-Crick base pair at that point)


Arginine tRNA synthetase complex with Arg-tRNA 1f7v

Drag the structure with the mouse to rotate

ReferencesReferences

  1. ↑ Cavarelli J, Moras D. Recognition of tRNAs by aminoacyl-tRNA synthetases. FASEB J. 1993 Jan;7(1):79-86. PMID:8422978
  2. ↑ Jin D, Wek SA, Kudlapur NT, Cantara WA, Bakhtina M, Wek RC, Musier-Forsyth K. Disease-associated mutations in a bifunctional aminoacyl-tRNA synthetase gene elicit the integrated stress response. J Biol Chem. 2021 Oct;297(4):101203. PMID:34537243 doi:10.1016/j.jbc.2021.101203
  3. ↑ Zhang CM, Liu C, Slater S, Hou YM. Aminoacylation of tRNA with phosphoserine for synthesis of cysteinyl-tRNA(Cys). Nat Struct Mol Biol. 2008 May;15(5):507-14. PMID:18425141 doi:10.1038/nsmb.1423

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