Structure of PDB 1nyr Chain B

Receptor sequence
>1nyrB (length=637) Species: 1280 (Staphylococcus aureus) [Search protein sequence]
MEQINIQFPDGNKKAFDKGTTTEDIAQSISPGLRKKAVAGKFNGQLVDLT
KPLETDGSIEIVTPGSEEALEVLRHSTAHLMAHAIKRLYGNVKFGVGPVI
EGGFYYDFDIDQNISSDDFEQIEKTMKQIVNENMKIERKVVSRDEAKELE
LIDAIPEDENVTLYSQGDFTDLCRGVHVPSTAKIKEFKLLSTAGAYWRGD
SNNKMLQRIYGTAFFDKKELKAHLQMLEERKERDHRKIGKELELFTNSQL
VGAGLPLWLPNGATIRREIERYIVDKEVSMGYDHVYTPVLANVDLYKTSG
HWDHYQEDMFPPMQLDETESMVLRPMNCPHHMMIYANKPHSYRELPIRIA
ELGTMHRYEASGAVSGLQRVRGMTLNDSHIFVRPDQIKEEFKRVVNMIID
VYKDFGFEDYSFRLSYRDPEDKEKYFDDDDMWNKAENMLKEAADELGLSY
EEAIGEAAFYGPKLDVQVKTAMGKEETLSTAQLDFLLPERFDLTYIGQDG
EHHRPVVIHRGVVSTMERFVAFLTEETKGAFPTWLAPKQVQIIPVNVDLH
YDYARQLQDELKSQGVRVSIDDRNEKMGYKIREAQMQKIPYQIVVGDKEV
ENNQVNVRQYGSQDQETVEKDEFIWNLVDEIRLKKHR
3D structure
PDB1nyr Conformational movements and cooperativity upon amino acid, ATP and tRNA binding in threonyl-tRNA synthetase
ChainB
Resolution2.8 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) C336 R365 L383 D385 H387 K471 H517
Catalytic site (residue number reindexed from 1) C328 R357 L375 D377 H379 K463 H509
Enzyme Commision number 6.1.1.3: threonine--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 ZN B C336 H387 H517 C328 H379 H509
BS02 ATP B R365 R377 V378 M381 S522 T523 R526 R357 R369 V370 M373 S514 T515 R518
BS03 THR B M334 C336 D385 H517 M326 C328 D377 H509
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004829 threonine-tRNA ligase activity
GO:0005524 ATP binding
GO:0016740 transferase activity
GO:0046872 metal ion binding
Biological Process
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006435 threonyl-tRNA aminoacylation
GO:0043039 tRNA aminoacylation
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1nyr, PDBe:1nyr, PDBj:1nyr
PDBsum1nyr
PubMed12875846
UniProtQ8NW68|SYT_STAAW Threonine--tRNA ligase (Gene Name=thrS)

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