Structure of PDB 4dpg Chain D

Receptor sequence

>4dpgD (length=505) Species: 9606 (Homo sapiens)

VDPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDH
LTDITLKVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFI
HINNKLRRGDIIGVQGNPGKTKKGELSIIPYEITLLSPCLHMLPHLHFGL
KDKETRYRQRYLDLILNDFVRQKFIIRSKIITYIRSFLDELGFLEIETPM
MNIIPGGAVAKPFITYHNELDMNLYMRIAPELYHKMLVVGGIDRVYEIGR
QFRNEGIDLTHNPEFTTCEFYMAYADYHDLMEITEKMVSGMVKHITGSYK
VTYHPDGPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETR
KILDDICVAKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMS
PLAKWHRSKEGLTERFELFVMKKEICNAYTELNDPMRQRQLFEEQAKAKA
AGDDEAMFIDENFCTALEYGLPPTAGWGMGIDRVAMFLTDSNNIKEVLLF
PAMKP

3D structure

• PDB: 4dpg Structural Switch of Lysyl-tRNA Synthetase between Translation and Transcription.
• Chain: D
• 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): R253 E255 T260 H261 E424 N427 R483
• 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	D	G277 E301 E339 Y341 N497 Y499 E501 G546	G207 E231 E269 Y271 N427 Y429 E431 G476
BS02	APC	D	R323 T330 H331 N332 F335 E494 R553 I564	R253 T260 H261 N262 F265 E424 R483 I494
BS03	MG	D	E487 E494	E417 E424

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)