Structure of PDB 1ivs Chain B

Receptor sequence

>1ivsB (length=862) Species: 274 (Thermus thermophilus) [Search protein sequence]

MDLPKAYDPKSVEPKWAEKWAKNPFVANPKSGKPPFVIFMPPPNVTGSLH
MGHALDNSLQDALIRYKRMRGFEAVWLPGTDHAGIATQVVVERLLLKEGK
TRHDLGREKFLERVWQWKEESGGTILKQLKRLGASADWSREAFTMDEKRS
RAVRYAFSRYYHEGLAYRAPRLVNWCPRCETTLSDLEVETEPTPGKLYTL
RYEVEGGGFIEIATVRPETVFADQAIAVHPEDERYRHLLGKRARIPLTEV
WIPILADPAVEKDFGTGALKVTPAHDPLDYEIGERHGLKPVSVINLEGRM
EGERVPEALRGLDRFEARRKAVELFREAGHLVKEEDYTIALATCSRCGTP
IEYAIFPQWWLRMRPLAEEVLKGLRRGDIAFVPERWKKVNMDWLENVKDW
NISRQLWWGHQIPAWYCEDCQAVNVPRPERYLEDPTSCEACGSPRLKRDE
DVFDTWFSSALWPLSTLGWPEETEDLKAFYPGDVLVTGYDILFLWVSRME
VSGYHFMGERPFKTVLLHGLVLDEKGQKMSKSKGNVIDPLEMVERYGADA
LRFALIYLATGGQDIRLDLRWLEMARNFANKLYNAARFVLLSREGFQAKE
DTPTLADRFMRSRLSRGVEEITALYEALDLAQAAREVYELVWSEFCDWYL
EAAKPALKAGNAHTLRTLEEVLAVLLKLLHPMMPFLTSELYQALTGKEEL
ALEAWPEPGGRDEEAERAFEALKQAVTAVRALKAEAGLPPAQEVRVYLEG
ETAPVEENLEVFRFLSRADLLPERPAKALVKAMPRVTARMPLEGLLDVEE
WRRRQEKRLKELLALAERSQRKLASPGFREKAPKEVVEAEEARLKENLEQ
AERIREALSQIG

3D structure

PDB

1ivs Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase

Chain

Resolution

2.9 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)	C176 C179 C344 C347 W456 I491 W495 K528 K531
Catalytic site (residue number reindexed from 1)	C176 C179 C344 C347 W456 I491 W495 K528 K531
Enzyme Commision number	6.1.1.9: valine--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	B	A213 T214 V215 E261 F264 L269 L278 E281 Y337 R385 T560 Q563 R566 D568 R570 W571 M574 N577 N580 K581 N584 A585 R587 F588 R635 C646 L650 K654 R730 P740 A741 R767 R818 P826 G827 F828 K831 A832 P833 V836 R843	A213 T214 V215 E261 F264 L269 L278 E281 Y337 R385 T560 Q563 R566 D568 R570 W571 M574 N577 N580 K581 N584 A585 R587 F588 R635 C646 L650 K654 R730 P740 A741 R767 R818 P826 G827 F828 K831 A832 P833 V836 R843
BS02	VAA	B	P41 P42 N44 H50 G52 H53 D56 D81 W456 S459 T487 G488 D490 I491 W495 H518 L520 V521 M529	P41 P42 N44 H50 G52 H53 D56 D81 W456 S459 T487 G488 D490 I491 W495 H518 L520 V521 M529

Gene Ontology

	Molecular Function
GO:0000166	nucleotide binding
GO:0002161	aminoacyl-tRNA editing activity
GO:0004812	aminoacyl-tRNA ligase activity
GO:0004832	valine-tRNA ligase activity
GO:0005524	ATP binding
GO:0046872	metal ion binding

	Biological Process
GO:0006412	translation
GO:0006418	tRNA aminoacylation for protein translation
GO:0006438	valyl-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:1ivs, PDBe:1ivs, PDBj:1ivs
PDBsum	1ivs
PubMed	12554880
UniProt	P96142\|SYV_THETH Valine--tRNA ligase (Gene Name=valS)

[Back to BioLiP]