Structure of PDB 4dpg Chain E

Receptor sequence

>4dpgE (length=500) Species: 9606 (Homo sapiens)

DPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDHL
TDITLKVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFIH
INNKLRRGDIIGVQGNPGKTKKGELSIIPYEITLLSPCLHMLPHLKDKET
RYRQRYLDLILNDFVRQKFIIRSKIITYIRSFLDELGFLEIETPMMNIIP
GGAVAKPFITYHNELDMNLYMRIAPELYHKMLVVGGIDRVYEIGRQFRNE
GIDLTHNPEFTTCEFYMAYADYHDLMEITEKMVSGMVKHITGSYKVTYHP
DGPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETRKILDD
ICVAKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSPLAKW
HRSKEGLTERFELFVMKKEICNAYTELNDPMRQRQLFEEQAKAKAAGDDE
AMFIDENFCTALEYGLPPTAGWGMGIDRVAMFLTDSNNIKEVLLFPAMKP

3D structure

• PDB: 4dpg Structural Switch of Lysyl-tRNA Synthetase between Translation and Transcription.
• Chain: E
• Resolution: 2.844 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): R323 E325 T330 H331 E494 N497 R553
• Catalytic site (residue number reindexed from 1): R248 E250 T255 H256 E419 N422 R478
• Enzyme Commision number: 2.7.7.-
  6.1.1.6: lysine--tRNA ligase.

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	LYS	E	E301 E339 Y341 N497 Y499 E501 G546	E226 E264 Y266 N422 Y424 E426 G471
BS02	APC	E	R323 T330 H331 N332 F335 R553	R248 T255 H256 N257 F260 R478
BS03	MG	E	E487 E494	E412 E419

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003676 nucleic acid binding
• GO:0004812 aminoacyl-tRNA ligase activity
• GO:0004824 lysine-tRNA ligase activity
• GO:0005524 ATP binding

Biological Process

• GO:0006418 tRNA aminoacylation for protein translation
• GO:0006430 lysyl-tRNA aminoacylation

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:4dpg, PDBe:4dpg, PDBj:4dpg
• PDBsum: 4dpg
• PubMed: 23159739
• UniProt: Q15046|SYK_HUMAN Lysine--tRNA ligase (Gene Name=KARS1)