Structure of PDB 5onh Chain D

Receptor sequence

>5onhD (length=860) Species: 83333 (Escherichia coli K-12) [Search protein sequence]

MQEQYRPEEIESKVQLHWDEKRTFEVTEDESKEKYYCLSMLPYPSGRLHM
GHVRNYTIGDVIARYQRMLGKNVLQPIGWDAFGLPAEGAAVKNNTAPAPW
TYDNIAYMKNQLKMLGFGYDWSRELATCTPEYYRWEQKFFTELYKKGLVY
KKTSAVNWCPNDQTVLANEQVIDGCCWRCDTKVERKEIPQWFIKITAYAD
ELLNDLDKLDHWPDTVKTMQRNWIGRSEGVEITFNVNDYDNTLTVYTTRP
DTFMGCTYLAVAAGHPLAQKAAENNPELAAFIDECRNTKVAEAEMATMEK
KGVDTGFKAVHPLTGEEIPVWAANFVLMEYGTGAVMAVPGHDQRDYEFAS
KYGLNIKPVILAADGSEPDLSQQALTEKGVLFNSGEFNGLDHEAAFNAIA
DKLTAMGVGERKVNYRLRDWGVSRQRYWGAPIPMVTLEDGTVMPTPDDQL
PVILPEDVVMDGITSPIKADPEWAKTTVNGMPALRETDTFDTFMESSWYY
ARYTCPQYKEGMLDSEAANYWLPVDIYIGGIEHAIMHLLYFRFFHKLMRD
AGMVNSDEPAKQLLCQGMVLADAFYYVGENGERNWVSPVDAIVERDEKGR
IVKAKDAAGHELVYTGMSKMSKSKNNGIDPQVMVERYGADTVRLFMMFAS
PADMTLEWQESGVEGANRFLKRVWKLVYEHTAKGDVAALNVDALTENQKA
LRRDVHKTIAKVTDDIGRRQTFNTAIAAIMELMNKLAKAPTDGEQDRALM
QEALLAVVRMLNPFTPHICFTLWQELKGEGDIDNAPWPVADEKAMVEDST
LVVVQVNGKVRAKITVPVDATEEQVRERAGQEHLVAKYLDGVTVRKVIYV
PGKLLNLVVG

3D structure

PDB

5onh Kinetic Origin of Substrate Specificity in Post-Transfer Editing by Leucyl-tRNA Synthetase.

Chain

Resolution

3.1 Å

3D
structure

Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]

Enzymatic activity

Catalytic site (original residue number in PDB)	F493 H533 F543 K619 K622
Catalytic site (residue number reindexed from 1)	F493 H533 F543 K619 K622
Enzyme Commision number	6.1.1.4: leucine--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	rna	D	D80 G83 L84 A167 N168 E169 M219 N222 W223 E292 A293 T297 R416 L417 R418 R424 R426 F493 E532 H533 L570 G616 M617 S618 K619 F648 A649 P651 Q659 G665 R668 K711 R719 N723 T724 M730 E731 N734 L801 V803 V810 R811 K813 V850 L854	D80 G83 L84 A167 N168 E169 M219 N222 W223 E292 A293 T297 R416 L417 R418 R424 R426 F493 E532 H533 L570 G616 M617 S618 K619 F648 A649 P651 Q659 G665 R668 K711 R719 N723 T724 M730 E731 N734 L801 V803 V810 R811 K813 V850 L854
BS02	ZN	D	C159 C176 C179	C159 C176 C179
BS03	LSS	D	M40 L41 P42 Y43 G51 H52 N55 S496 G530 E532 H533 H537 Q566 M568 V569	M40 L41 P42 Y43 G51 H52 N55 S496 G530 E532 H533 H537 Q566 M568 V569	BindingDB: Ki=0.139000nM
BS04	VRT	D	T247 T248 R249 Y330 V335 M336 R344	T247 T248 R249 Y330 V335 M336 R344

Gene Ontology

	Molecular Function
GO:0000166	nucleotide binding
GO:0002161	aminoacyl-tRNA editing activity
GO:0004812	aminoacyl-tRNA ligase activity
GO:0004823	leucine-tRNA ligase activity
GO:0005515	protein binding
GO:0005524	ATP binding

	Biological Process
GO:0006412	translation
GO:0006418	tRNA aminoacylation for protein translation
GO:0006429	leucyl-tRNA aminoacylation
GO:0106074	aminoacyl-tRNA metabolism involved in translational fidelity

	Cellular Component
GO:0005737	cytoplasm
GO:0005829	cytosol

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:5onh, PDBe:5onh, PDBj:5onh
PDBsum	5onh
PubMed	29111343
UniProt	P07813\|SYL_ECOLI Leucine--tRNA ligase (Gene Name=leuS)

[Back to BioLiP]