Structure of PDB 3a2k Chain A

Receptor sequence

>3a2kA (length=462) Species: 1462 (Geobacillus kaustophilus)

MIDKVRAFIHRHQLLSEGAAVIVGVSGGPDSLALLHVFLSLRDEWKLQVI
AAHVDHMFRGRESEEEMEFVKRFCVERRILCETAQIDVPAFQRSAGLGAQ
EAARICRYRFFAELMEKHQAGYVAVGHHGDDQVETILMRLVRGSTSKGYA
GIPVKRPFHGGYLIRPFLAVSRAEIEAYCRQMGLSPRCDPSNEKDDYTRN
RFRHHIVPLLRQENPRLHERFQQYSEMMAEDEQFLEELAADALNKVMEKQ
HRDAALSIGPFLELPRPLQRRVLQLLLLRLYGGVPPTLTSVHIGHILMLC
ERGRPSGMIDLPKGLKVIRSYDRCLFTFDAESGEKGYWFELPVPALLPLP
NGYAIISEFGEHYPRKQAGNDWFVVDPASVSLPLRVRTRRRGDRMVLKGT
GGTKKLKEIFIEAKIPRMERDRWPIVEDADGRILWVPGLKKSAFEAQNRG
QARYILLQYQAM

3D structure

• PDB: 3a2k Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase.
• Chain: A
• Resolution: 3.65 Å

Enzymatic activity

• Enzyme Commision number: 6.3.4.19: tRNA(Ile)-lysidine synthetase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	A	Q100 E101 R104 R107 Y108 H127 R139 R142 G143 S144 I152 R156 R165 T198 R199 Q274 G283 T287 L288 T289 S290 H292 R302 S306 M308 D310 L311 R389 R391 R394 G399 G401 T403 K404 K405 K407 I411 E412 K414 R420 K440	Q100 E101 R104 R107 Y108 H127 R139 R142 G143 S144 I152 R156 R165 T198 R199 Q274 G283 T287 L288 T289 S290 H292 R302 S306 M308 D310 L311 R389 R391 R394 G399 G401 T403 K404 K405 K407 I411 E412 K414 R420 K440
BS02	rna	A	N214 R216	N214 R216

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0005524 ATP binding
• GO:0016874 ligase activity
• GO:0016879 ligase activity, forming carbon-nitrogen bonds
• GO:0032267 tRNA(Ile)-lysidine synthase activity

Biological Process

• GO:0006400 tRNA modification
• GO:0008033 tRNA processing

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:3a2k, PDBe:3a2k, PDBj:3a2k
• PDBsum: 3a2k
• PubMed: 19847269
• UniProt: Q5L3T3|TILS_GEOKA tRNA(Ile)-lysidine synthase (Gene Name=tilS)