Aminoacyl tRNA Synthetase

File:3l4g.png

Crystal Structure of Aminoacyl tRNA synthetase 3l4g

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).

3D Structures of Aminoacyl tRNA synthetase3D Structures of Aminoacyl tRNA synthetase

Updated on 02-October-2013

Class I aaRS
==========

Arg-RSArg-RS

1bs2 – yArgRS
3gdz – ArgRS residues 1-106 – Klebsiella pneumoniae
1iq0 – TtArgRS - Thermus thermophilus

Arg-RS + tRNA

2zuf - PhArgRS + Arg-tRNA - Pyrococcus horikoshii
1f7v - yArgRS + Arg-tRNA

Arg-RS ternary complex

1f7u – yArgRS + Arg-tRNA + Arg
2zue – PhArgRS + Arg-tRNA + ATP analog

Cys-RSCys-RS

1li5 - EcCysRS - Escherichia coli
1li7 - EcCysRS + Cys
1u0b – EcCysRS + Cys-tRNA

Gln-RSGln-RS

1nyl– EcGlnRS
2gls, 1lgr – StGlnRS – Salmonella typhimurium
2lgs – StGlnRS + Glu
1qrt, 1qru, 1qrs - EcGlnRS (mutant) + Gln-tRNA
1gtr, 1gts, 1gsg - EcGlnRS + Gln-tRNA
1qtq - EcGlnRS + Gln-tRNA + Gln analog

Gln-RS ternary complex

1euq, 1euy – EcGlnRS + Gln-tRNA + Gln-SA
1exd - EcGlnRS + Gln-tRNA (mutant) + AMP

Glu-RSGlu-RS

1gln – TtGluRS
2o5r - TmGluRS
3aii – GluRS – Methanothermobacter thermautotrophicus
2ja2 – MtGluRS – Mycobacterium tuberculosis
2zlz – EcGluRS
2hz7 – DrGluRS – Deinococcus radiodurans
2hra – yGluRS N-terminal

Glu-RS + small substrates or analogs

3afh - TmGluRS + Glu-AMP analog
2rd2, 2re8 – EcGluRS (mutant) + Glu-SA
2cuz – TtGluRS + Glu
1j09 - TtGluRS + Glu + ATP
1n75 - TtGluRS + ATP
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
1o0b, 1o0c - EcGluRS + Glu-tRNA + Glu + AMP
2cv0, 1n77 - TtGluRS + Glu + Glu-tRNA
1n78 - TtGluRS + Glu-ol + Glu-tRNA
2cv1 - TtGluRS + Glu-ol + ATP + Glu-tRNA
2cv2 - TtGluRS + Glu-SA + Glu-tRNA
2hrk, 2hsm - yGluRS N-terminal + GU4 nucleic-binding protein 1

Ile-RSIle-RS

1ile - TtIleRS
1wny, 1udz – TtIleRS editing domain

Ile-RS + small substrates or analogs

1ue0 - TtIleRS editing domain + Val
1wnz - TtIleS editing domain + Val-adenylate
1wk8 - TtIleRS editing domain + Val-SA
1jzq – TtIleS + Ile-adenylate analog
1jzs – TtIleS + antibiotic

Ile-RS ternary complex

1ffy, 1qu2, 1qu3 - SaIleRS + Ile-tRNA + antibiotic - Staphylococcus aureus

Leu-RSLeu-RS

3o0a – AaLeuRS hydrolytic domain – Aquifex aeolicus
2wfd – hLeuRS editing domain – human
2wfe - CaLeuRS editing domain – Candida albicans
2ajg - EcLeuRS editing domain
1wkb – PhLeuRS residues 1-810

Leu-RS + small substrates or analogs

2wfg - CaLeuRS editing domain + benzoxaborole-AMP
2v0c – TtLeuRS + Leu-SA + benzoxaborole-AMP
1h3n - TtLeuRS + Leu-SA
1obc, 1obh – TtLeuRS + substrate analog
2ajh, 2aji - EcLeuRS editing domain + aa

Leu-RS + tRNA

1wz2 – PhLeuRS Leu-tRNA

Leu-RS ternary complex

2v0g - TtLeuRS + Leu-tRNA + benzoxaborole-AMP
2bte, 2byt - TtLeuRS + Leu-tRNA + Leu

Lys-RSLys-RS

1irx – PhLysRS
1bbw – EcLysRS
1krs, 1krt – EcLysRS anticodon-binding domain – NMR
3dsq – DhLysRS – Desulfitobacterium hafniense
2e3c - MmLysRS catalytic domain - Methanosarcina mazei
3bju – hLysRS residues 70-579

Lys-RS + small substrates or analogs

3a74 – GsLysRS + diadenosine tetraphosphate – Geobacillus stearothermophilus
3e9h, 3e9i – BsLysRS + Lys-SA - Bacillus stearothermophilus
2zin – MmLysRS catalytic domain + Boc-Lys + ATP analog
2zio - MmLysRS catalytic domain + Aloc-Lys-AMP + PNP
2zcd - MmLysRS catalytic domain + AMPPNP
2zce - MmLysRS catalytic domain + pyrro-Lys + ATP analog
2zim - MmLysRS residues 185-454+ pyrro-Lys-adenylate
2q7e - MmLysRS C-terminal + ATP analog
2q7g - MmLysRS C-terminal+ pyrro-Lys analog+ ATP
1bbu, 1e10, 1lyl – EcLysRS + Lys
1e1t - EcLysRS + Lys-adenylate
1e22 - EcLysRS + Lys + AMPPCP
1e24 - EcLysRS + Lys + ATP

Leu-RS + tRNA

2zni, 2znj – DhLysRS + tRNA

Met-RSMet-RS

1a8h – TtMetRS
1med, 1mea – EcMetRS Zinc-binding domain - NMR
1qqt - EcMetRS residues 2-552
2x1l - MsMetRS residues 2-515 – Mycobacterium smegmatis
3h97 – EcMetRS residues 2-548 (mutant)
3h9c - EcMetRS residues 2-548
2d54, 2d5b – TtMetRS (mutant)
1woy – TtMetRS residues 1-500 (mutant)
2djv – hMetRS WHEP-TRS domain – NMR
1pyb – AaMetRS β subunit
1rqg – PaMetRS – Pyrococcus abyssi
1mkh – PaMetRS C-terminal

Met-RS + small substrates or analogs

3kfl – LmMetRS residues 206-747+ Met-adenylate - Leishmania major
2x1m - MsMetRS residues 2-515 + Met
1p7p, 1pfu, 1pfv, 1pfw - EcMetRS residues 2-548 + Met
1pfy - EcMetRS residues 1-551 + Met-SA
1f4l - EcMetRS residues 1-551 + Met
1pg0 - EcMetRS residues 1-551 + Met-adenylate
1pg2 - EcMetRS residues 1-551 + Met + adenine
3h99 - EcMetRS residues 2-548 (mutant) + Met
3h9b - EcMetRS residues 2-548 (mutant) + azidonorleucine
4dlp - MetRS + SMet – Brucella melitensis

Met-RS + tRNA

2csx – AaMetRS + Met-tRNA

Met-RS + tRNA

2ct8 - AaMetRS + Met-tRNA + Met-SA
2dxi – TtMetRS + tRNA + ATP + Glu-ol

2hsn - yMetRS N-terminal + GU4 nucleic-binding protein 1 N-terminal

Trp-RSTrp-RS

1d2r - GsTrpRS
3prh – TrpRS (mutant) – Bacillus subtilis
3n9i – TrpRS – Yarsinia pestis
3m5w – CjTrpRS – Campylobacter jejuni
3a04 – ApTrpRS – Aeropyrum pernix
3hzr – EhTrpRS – Entamoeba histolytica
3i05 – TbTrpRS residues 3-389 – Trypanosoma brucei
3hv0 – TRrpS residues 206-593 – Cryptosporidium parvum
3foc – GlTrpRS – Giardia lamblia
1o5t – hTrpRS catalytic fragment
1ulh – hTrpRS residues 35-424
2el7 – TtTrpRS
2ip1, 3kt0 – yTrpRS – yeast
2yy5 – TrpRS – Mycoplasma pneumoniae
2g36 – TmTrpRS
1bks – StTrpRS + pyridoxal phosphate

Trp-RS + small substrates or analogs

3a05 – ApTrpRS + Trp
3kt3 – yTrpRS + Trp-adenylate
3kt6, 3kt8 – yTrpRS + Trp
3jxe – PhTrpRS + Trp-adenylate
3fhj, 3fio – BsTrpRS + Trp + AMP + Pi
2quh – hTrpRS + Trp
2qui - hTrpRS + Trp-amide + ATP
2quj - hTrpRS + Trp-adenylate
2quk – hTrpRS + ATP
2ov4 – GsTrpRS + adenosine tetraphosphate
1i6k, 1i6l, 1i6m – GsTrpRS + Trp-adenylate
1yid, 2a4m – DrTrpRS + ATP
1yi8, 1yia – DrTrpRS + Trp
1mau – GsTrpRS + Trp + ATP
1maw, 1m83 - GsTrpRS + ATP
1mb2 - GsTrpRS + Trp
3tze - TrpRS + Trp - Encephalitozoon cuniculi
3tzl - CjTrpRS + Trp + ADP
3sz3 - TrpRS + Trp - Vibrio cholerae

Trp-RS + tRNA

2azx – hTrpRS (mutant) + tRNA
2ake, 2dr2 - hTrpRS + Trp-tRNA

Tyr-RSTyr-RS

1tya, 1tyb, 1tyc, 1tyd, 2ts1 – GsTyrRS
3qe4, 3d6u, 3d6v, 2pxh, 2hgz, 1u7d – MjTyrRS – Methanocaldococcus jannaschii
1u7x, 4hjr, 4hk4- MjTyrRS (mutant)
2jan – MtTyrRS
1y42 - NcTyrRS – Neurospora crassa
2cya – ApTyrRS
1n3l - hTyrRS residues 1-364
1r6t, 1r6u – yTyrRS (mutant)
1jh3 – GsTyrRS C-terminal – NMR

Tyr-RS + small substrates or analogs

3ts1 – GsTyrRS + Tyr-adenylate intermediate
4ts1 – GsTyrRS + Tyr
3p0h, 3p0i, 3p0j – LmTyrRS + inhibitor
3n2y – MjTyrRS + tetrazolyl phenylalanine
2zp1 – MjTyrRS (mutant) + Tyr
1zh0 - MjTyrRS (mutant) + naphthyl-Ala
1zh6 - MjTyrRS (mutant) + acetyl-Phe
2ag6 - MjTyrRS (mutant) + bromo-Phe
4hjx - MjTyrRS (mutant) + di-fluoro-Tyr
2yxn – EcTyrRS residues 1-322 + azido-Tyr
1vbm – EcTyrRS + Tyr-SA
1vbn – EcTyrRS (mutant) + Tyr-SA
1wq3, 1wq4 - EcTyrRS (mutant) + Tyr
1x8x – EcTyrRS + Tyr
2pid – hTyrRS residues 28-375 + Tyr-SA
2j5b – TyrRS residues 2-346 + Tyr-ol – Acanthamoeba polyphaga minivirus
2dlc – yTyrRS + tRNA + Tyr-SA
2cyb – AfTyrRS + Tyr - Archaeoglobus fulgidus
2cyc – PhTyrRS + Tyr
1q11 – hTyrRS residues 1-364 + Tyr-ol
1h3e - TtTyrRS + Tyr-tRNA + Tyr-ol + ATP
1h3f - TtTyrRS + Tyr-ol
1jh3 – GsTyrRS C-terminal – NMR
1jii, 1jij, 1jil, 1jik – SaTyrRS + inhibitor

Tyr-RS + tRNA

1j1u – MjTyrRS + Tyr-tRNA

2rkj – NcTyrRS + RNA

Val-RSVal-RS

1iyw - TtValRS
1wk9, 1wka – TtValRS CP1 domain

Val-RS ternary complex

1ivs – TtValRS + Val-SA + Val-tRNA
1gax - TtValRS + Val-adenylate analog + Val-tRNA

Class II aaRS
==========

Ala-RSAla-RS

3g98 – AaAlaRS residues 758-867
1riq - AaAlaRS catalytic fragment
2zze, 2zzf, 1wnu, 1wxo, 1v4p – PhAlaRS
2zvf – AfAlaRS C-terminal

Ala-RS + small substrates or analogs

3hxu, 3hxv, 3hxw – EcAlaRS catalytic fragment + aa-adenylate
3hxz, 3hy0, 3hy1 - EcAlaRS catalytic fragment (mutant) + aa-adenylate
3hxx - EcAlaRS catalytic fragment + AMPPCP
3hxy - EcAlaRS catalytic fragment + AMPPCP + Ala-AMP + PCP
3htz - AaAlaRS residues 2-454 + Ser
1yfr – AaAlaRS + ATP
1yfs – AaAlaRS + Ala
1yft, 1ygb - AaAlaRS catalytic fragment + aa
2zzg - PhAlaRS + Ala-SA
2ztg – AfAlaRS + Ala-SA

Asp-RSAsp-RS

3nen, 1b8a – TkAspRS - Thermococcus kodakarensis
3i7f – EhAspRS
1wyd– AspRS – Sulfolobus tokodaii
1eov - yAspRS
1n9w, 1l0w, 1g51 – TtAspRS
1eqr – EcAspRS

Asp-RS + small substrates or analogs

3nel – TkAspRS + Asp
3nem - TkAspRS + Asp-adenylate

Asp-RS + tRNA

3kfu, 1efw – TtAspRS + tRNA
1asy, 1asz – yAspRS + Asp-tRNA

Asp-RS ternary complex

1il2, 1c0a – EcAspRS + Asp-tRNA + Asp-adenylate

Asn-RSAsn-RS

1x56 - PhAsnRS
2kqr – BmAsnRS N-terminal – NMR – Brugia malayi

Asn-RS + small substrates or analogs

2xti – BmAsnRS catalytic fragment + Asn-adenine analog
2xgt - BmAsnRS catalytic fragment + Asn-SA
1x54 – PhAsnRS + Asn-adenylate
1x55 - PhAsnRS + Asn-SA
11as – EcAsnRS + Asn
12as - EcAsnRS + Asn + AMP

Gly-RSGly-RS

1ati – TtGlyRS
2q5h – hGlyRS residues 55-739
2q5i - hGlyRS residues 55-739 (mutant)
2pme – hGlyRS
2pmf – hGlyRS (mutant)
1j5w – TmGlyRS α chain

Gly-RS + small substrates or analogs

2zt5, 2zxf – hGlyRS residues 55-739 + bis-adenosine tetraphosphate
2zt6 - hGlyRS residues 55-739 + AMPCPP
2zt7 - hGlyRS residues 55-739 + Gly + ATP
2zt8 - hGlyRS residues 55-739 + Gly-AMP analog
1b76 – TtGlyRS + ATP
1ggm – TtGlyRS + Gly-adenylate

His-RSHis-RS

1htt - EcHisRS
3net – HisRS – Nostoc
1h4v – TtHisRS
1qe0 – SaHisRS
3hri – TbHisRS
1wu7 – HisRS – Thermoplasma acidophilum
1x59 – hHisRS WHEP-TRS domain - NMR

His-RS + small substrates or analogs

3lc0 – HisRS residues 45-478 + His – Trypanosoma cruzi
1adj – TtHisRS + His
3hrk - TbHisRS + His-adenylate
2el9 - EcHisRS + His-SA
1kmm, 1ady - EcHisRS + His-adenylate
1kmn - EcHisRS + His-ol + ATP

Phe-RSPhe-RS

1pys – TtPheRS
3l4g, 3cmq – hPheRS
2cxi – PhPheRS β chain N-terminal
3ica – PheRS β chain – Porphyromonas gingivalis

Phe-RS + small substrates or analogs

3pco – EcPheRS + phenylalanine+ AMP
3hfz, 2amc – TtPheRS α+β chains + Tyr
2akw, 1b70 - TtPheRS α+β chains + Phe
1jjc, 1b7y - TtPheRS α+β chains + Phe-adenylate
2aly - TtPheRS α+β chains + Phe-SA
2rhq, 2rhs – PheRS α+β chains (mutant) + inhibitor – Staphylococcus haemolyticus

Phe-RS + tRNA

1eiy - TtPheRS α+β chains + Phe-tRNA

Phe-RS ternary complex

2iy5 - TtPheRS α+β chains + Phe-ol + Phe-tRNA

Pro-RSPro-RS

1hc7 – TtProRS
2i4l – RpProRS – Rhodopseudomonas palustris
1nj2 - MtProRS – Methanothermobacter thermautotrophicus
1nj8 – MjProRS

Pro-RS + small substrates or analogs

3ial – GlProRS residues 34-542 + Pro-adenylate
2i4m, 2i4n – RpProRS + aa-SA
2i4o – RpProRS + ATP
2j3l – EfProRS + Pro-SA – Enterococcus faecalis
2j3m – EfProRS + Pro-ol + ATP
1nj1, 1nj5, 1nj6 – MtProRS + aa-SA
1h4t - TtProRS + Pro

Pro-RS ternary complex

1h4q - TtProRS + Pro-tRNA + Pro-ol
1h4s - TtProRS + Pro-tRNA + Pro-SA

Ser-RSSer-RS

3lsq – TbSerRS
1sry - TtSerRS
3err – TtSerRS/dynein heavy chain
2zr3 – PhSerRS
2dq3 – AaSerRS
2du7 – MjSerRS
2odr – SerRS – Methanococcus maripaludis
2cim – MbSerRS – Methanosarcina barkeri
1wle – SerRS – bovine

Ser-RS + small substrates or analogs

2zr2 – PhSerRS + ATP
2dq0 – PhSerRS + Ser-SA
2cj9 – MbSerRS + Ser-SA
2cjb – MbSerRS + Ser
2cja – MbSerRS + ATP
1ses, 1set – TtSerRS + Ser-adenylate analog
3lss – TbSerRS + ATP

Ser-RS + tRNA

1ser – TtSerRS + Ser-tRNA
2du4 - AfSerRS + Cys-tRNA

Ser-RS ternary complex

2du3 – AfSerRS + Cys-tRNA + phosphoserine
2du5, 2du6 - AfSerRS (mutant) + Cys-tRNA + phosphoserine

Thr-RSThr-RS

1y2q - PaThrRS editing domain
1wwt – hThrRS TGS domain – NMR
1tje - EcThrRS editing domain

Thr-RS + small substrates or analogs

3pd2, 3pd3, 3pd4, 3pd5 – PaThrRS editing domain + aa-aminoadenosine
2hkz – PaThrRS editing domain + Ser
2hl0, 2hl1 - PaThrRS editing domain + Ser-adenylate
2hl2 - PaThrRS editing domain + Ser-SA
1tke - EcThrRS editing domain + Ser
1tkg - EcThrRS editing domain + Ser-SA
1tky - EcThrRS editing domain + Ser-adenylate
1fyf, 1evl - EcThrRS catalytic and anticodon-binding domains + aa-SA
1evk - EcThrRS catalytic and anticodon-binding domains + Thr
1nyq – SaThrRS + Thr-SA
1nyr – SaThrRS + ATP

Thr-RS + tRNA

1qf6 – EcThrRS + Thr-tRNA
1kog – EcThrRS catalytic and anticodon-binding domains + mRNA

Multifunctional RS

1fyj – hRS - NMR