X-ray diffraction and NMR structures of aminoacyl-tRNA synthetases

(September 2003)

Arginine

OrganismResolutionPDBBound moleculesNotesReference
Saccharomyces cerevisiae2.20Å1F7UtRNAArg, Arginine-Medline
Thermus thermophilus2.30Å1IQ0--Medline
Saccharomyces cerevisiae2.75Å1BS2--Medline
Saccharomyces cerevisiae2.90Å1F7VtRNAArg-Medline

Asparagine

OrganismResolutionPDBBound moleculesNotesReference
Escherichia coli2.50Å11ASL-Asparaginedimer, mutant C51A, C315ÅMedline
Escherichia coli2.20Å12ASL-Asparagine, AMP dimer, mutant C51A, C315ÅMedline

Aspartic acid

OrganismResolutionPDBBound moleculesNotesReference
Saccharomyces cerevisiae3.00Å1ASYtRNAAsp-Medline
Saccharomyces cerevisiae3.00Å1ASZtRNAAsp, ATP-Medline
Pyrococcus kodakaraensis1.90Å1B8A--Medline
Escherichia coli2.40Å1C0AtRNAAsp, aspartyl-adenylate-Medline
Escherichia coli2.60Å1IL2yeast tRNAAsp, aspartyl-adenylate -Medline
Escherichia coli2.70Å1EQR--Medline
Thermus thermophilus3.00Å1EFWE. coli tRNAAsp-Medline
Thermus thermophilus2.40Å1G51--Medline
Thermus thermophilus2.30Å1N9W-archaeal type non-dicriminatingMedline
Thermus thermophilus2.01Å1L0W-space grown crystalsMedline
Saccharomyces cerevisiae2.30Å1EOV-fragment w/o 70aa N-terminal domainMedline

Cysteine

OrganismResolutionPDBBound moleculesNotesReference
Escherichia coli2.30Å1LI5--Medline
Escherichia coli2.60Å1LI7Cys -Medline

Glutamine

OrganismResolutionPDBBound moleculesNotesReference
Escherichia coli3.10Å1EUQmutant tRNAGln,
Gln-AMP analog*
-Medline
Escherichia coli2.70Å1EXDtRNAGln aptamer-Medline
Thermus thermophilus2.50Å1GLN--Medline
Escherichia coli2.80Å1GSGtRNAGln, ATP -Medline
Escherichia coli2.50Å1GTRtRNA, ATP-Medline
Escherichia coli2.80Å1GTStRNA, AMP -Medline
Escherichia coli2.60Å1QRStRNAGlnmutant D235NMedline
Escherichia coli2.70Å1QRTtRNAGlnmutant D235GMedline
Escherichia coli3.00Å1QRUtRNAGlnmutant I129TMedline
Escherichia coli2.40Å1QTQtRNAGln,
Gln-AMP analog*
-Medline
Escherichia coli2.60Å1EUYmutant tRNAGln,
Gln-AMP analog*
-Medline
Escherichia coli2.60Å1NYL--Medline
Escherichia coli2.70Å1O0CL-glutamate,
ATP analog
-Medline
Escherichia coli2.70Å1O0BtRNAGln, L-glutamine,
ATP analog
-Medline

* 5'-O-[N-(L-glutaminyl)-sulfamoyl]adenosine - active site inhibitor

Glutamic acid

OrganismResolutionPDBBound moleculesNotesReference
Thermus thermophilus2.40Å1G59tRNAGlu-Medline
Thermus thermophilus1.80Å1J09Glutamic acid, ATP-Medline
Thermus thermophilus1.90Å1N75ATP-Medline
Thermus thermophilus2.40Å1N77tRNAGlu, ATP-Medline
Thermus thermophilus2.40Å1N78tRNAGlu, glutamol-AMP-Medline

Glutamic acid - proline

OrganismResolutionPDBBound moleculesNotesReference
Homo sapiensNMR1FYJ-Multifunctional peptide motif-1Medline

Glycine

OrganismResolutionPDBBound moleculesNotesReference
Thermotoga maritima1.95Å1J5W-alpha subunit-
Thermus thermophilus2.75Å1ATI--Medline
Thermus thermophilus3.40Å1B76ATP-Medline
Thermus thermophilus3.40Å1GGMglycyl-adenylate-Medline

Histidine

OrganismResolutionPDBBound moleculesNotesReference
Thermus thermophilus2.70Å1ADJhistidine-Medline
Thermus thermophilus2.80Å1ADYhistidyl-adenylate-Medline
Escherichia coli2.60Å1HTThistidyl-adenylate-Medline
Escherichia coli2.60Å1KMMhistidyl-adenylate-Medline
Escherichia coli2.80Å1KMNhistidinol, ATP-Medline
Staphylococcus aureus2.70Å1QE0--Medline
Thermus thermophilus2.40Å1H4V--Medline

Isoleucine

OrganismResolutionPDBBound moleculesNotesReference
Staphylococcus aureus2.20Å1FFYtRNAIle, mupirocin-Medline
Thermus thermophilus2.50Å1ILE--Medline
Thermus thermophilus3.00Å1JZQisoleucyl-adenylate analogue*--
Thermus thermophilus2.50Å1JZSmupirocin-Medline
Escherichia coli2.20Å1QU2tRNAIle, mupirocin--
Escherichia coli2.90Å1QU3tRNAIle, mupirocin--
* N-[isoleucinyl]-N'-[adenosyl]-diaminosulfone

Leucine

OrganismResolutionPDBBound moleculesNotesReference
Thermus thermophilus2.00Å1H3Nsulphamoyl analogue of leucyl-adenylate-Medline
Thermus thermophilus2.10Å1OBC--Medline
Thermus thermophilus2.20Å1OBH--Medline

Lysine

OrganismResolutionPDBBound moleculesNotesReference
Escherichia coli2.70Å1BBUlysine-Medline
Escherichia coli2.70Å1BBW--Medline
Escherichia coli2.12Å1E1Olysinehexagonal formMedline
Escherichia coli2.40Å1E1Tadenosine-5'-[lysyl-phosphate]-Medline
Escherichia coli2.43Å1E22lysine, ATP analoguehexagonal formMedline
Escherichia coli2.35Å1E24lysine, ATPhexagonal formMedline
Escherichia coliNMR1KRS-anticodon-binding domain 40-149, average structureMedline
Escherichia coliNMR1KRT-anticodon-binding domain 40-149,
9 structures
Medline
Escherichia coli2.80Å1LYLLysine -Medline
Pyrococcus horikoshii2.60Å1IRX-Class IMedline

Methionine

OrganismResolutionPDBBound moleculesNotesReference
Escherichia coliNMR1MEA-zinc binding domain 138-163, average structureMedline
Escherichia coliNMR1MED-zinc binding domain 138-163,
11 structures
Medline
Aquifex aeolicus2.50Å1PYB-beta subunitMedline
Escherichia coli1.85Å1F4Lmethionine-Medline
Escherichia coli2.03Å1QQT--Medline
Pyrococcus abyssi2.01Å1MKH-C-Terminal DomainMedline
Thermus thermophilus2.00Å1A8H---

Phenylalanine

OrganismResolutionPDBBound moleculesNotesReference
Thermus aquaticus2.70Å1B70phenylalanine-Medline
Thermus aquaticus2.50Å1B7Yphenylalaninyl-adenylate-Medline
Thermus thermophilus2.60Å1JJCphenylalanyl-adenylate-Medline
Thermus thermophilus3.30Å1EIYtRNAPhe-Medline
Thermus thermophilus2.90Å1PYS--Medline

Proline

OrganismResolutionPDBBound moleculesNotesReference
Methanocaldococcus janaschii3.20Å1NJ8--Medline
Methanothermobacter thermautotrophicus2.55Å1NJ1cysteine sulfamoyl adenylate-Medline
Methanothermobacter thermautotrophicus3.11Å1NJ2--Medline
Methanothermobacter thermautotrophicus2.80Å1NJ5proline sulfamoyl adenylate-Medline
Methanothermobacter thermautotrophicus2.85Å1NJ6alanine sulfamoyl adenylate-Medline
Thermus thermophilus3.00Å1H4QtRNAPro, ATP, prolinol-Medline
Thermus thermophilus2.85Å1H4StRNAPro, prolyl-adenylate analogue-Medline
Thermus thermophilus2.90Å1H4TL-proline-Medline
Thermus thermophilus2.43Å1HC7--Medline

Serine

OrganismResolutionPDBBound moleculesNotesReference
Thermus thermophilus2.90Å1SERtRNASer-Medline
Thermus thermophilus2.50Å1SESseryl-hydroxamate-AMP-Medline
Thermus thermophilus2.50Å1SETseryl-AMP analogue*-Medline
Thermus thermophilus2.50Å1SRY--Medline

* 5'-O-[N-(L-seryl)-sulphamoyl]adenosine

Threonine

OrganismResolutionPDBBound moleculesNotesReference
Escherichia coli2.50Å1EVKthreoninetruncated form 242-642Medline
Escherichia coli1.55Å1EVLthreonyl-adenylate analogue* truncated form 242-642Medline
Escherichia coli1.65Å1FYFseryl-adenylate analogue**truncated form 242-642Medline
Escherichia coli2.90Å1QF6tRNAThr, AMP-Medline
Escherichia coli3.50Å1KOGmRNA operator fragmentfragment 242-642Medline

* 5'-O-(N-(L-threonyl)-sulfamoyl)adenosine

** 5'-O-(N-(L-seryl)-sulfamoyl)adenosine

Tryptophan

OrganismResolutionPDBBound moleculesNotesReference
Bacillus stearothermophilus2.90Å1D2R--Medline
Bacillus stearothermophilus1.72Å1I6Ktryptophanyl-5'AMP -Medline
Bacillus stearothermophilus1.72Å1I6Ltryptophanyl-5'AMP -Medline
Bacillus stearothermophilus1.72Å1I6Mtryptophanyl-5'AMP -Medline
Bacillus stearothermophilus2.20Å1M83ATPclosed, pre-transition state conformationMedline
Bacillus stearothermophilus2.70Å1MAUtryptophanamide, ATPpre-transition state conformationMedline
Bacillus stearothermophilus3.00Å1MAWATPopen conformationMedline
Bacillus stearothermophilus2.70Å1MB2tryptophanopen conformationMedline

Tyrosine

OrganismResolutionPDBBound moleculesNotesReference
Bacillus stearothermophilusNMR1JH3-C-terminal domain, 20 structuresMedline
Bacillus stearothermophilus2.80Å1TYA-mutant T51A-
Bacillus stearothermophilus2.50Å1TYB->mutant T51G-
Bacillus stearothermophilus2.50Å1TYC-mutant T51P-
Bacillus stearothermophilus2.50Å1TYD-mutant T51SMedline
Bacillus stearothermophilus2.30Å2TS1tyrosinyl-adenylate-Medline
Bacillus stearothermophilus2.70Å3TS1tyrosinyl-adenylate -Medline
Bacillus stearothermophilus2.50Å4TS1tyrosinemutant del318-417Medline
Methanococcus jannaschii1.95Å1J1UtRNATyr, L-tyrosine -Medline
Homo sapiens2.21Å1NTG -Medline
Staphylococcus aureus3.20Å1JIISb219383-Medline
Staphylococcus aureus3.20Å1JIJSb239629-Medline
Staphylococcus aureus2.80Å1JIKSb243545-Medline
Staphylococcus aureus2.20Å1JILSb284485-Medline
Thermus thermophilus2.90Å1H3EtRNATyr, ATP, tyrosinol -Medline
Thermus thermophilus2.00Å1H3Ftyrosinol-Medline
Homo sapiens1.18Å1N3L-318 aa fragmentMedline

Valine

OrganismResolutionPDBBound moleculesNotesReference
Thermus thermophilus2.90Å1GAXtRNAVal, valyl-adenylate analogue*-Medline
Thermus thermophilus2.90Å1IVStRNAVal, valyl-adenylate analogue*-Medline
Thermus thermophilus4.00Å1IYW--Medline

* N-[valinyl]-N'-[adenosyl]-diaminosulfone