Structure of PDB 1ffy Chain A

Receptor sequence

>1ffyA (length=917) Species: 1280 (Staphylococcus aureus)

MDYEKTLLMPKTDFPMRGGLPNKEPQIQEKWDAEDQYHKALEKNKGNETF
ILHDGPPYANGNLHMGHALNKILKDFIVRYKTMQGFYAPYVPGWDTHGLP
IEQALTKKGVDRKKMSTAEFREKCKEFALEQIELQKKDFRRLGVRGDFND
PYITLKPEYEAAQIRIFGEMADKGLIYKGKKPVYWSPSSESSLAEAEIEY
HDKRSASIYVAFNVKDDKGVVDADAKFIIWTTTPWTIPSNVAITVHPELK
YGQYNVNGEKYIIAEALSDAVAEALDWDKASIKLEKEYTGKELEWVVAQH
PFLDRESLVINGDHVTTDAGTGCVHTAPGHGEDDYIVGQQYELPVISPID
DKGVFTEEGGQFEGMFYDKANKAVTDLLTEKGALLKLDFITHSYPHDWRT
KKPVIFRATPQWFASISKVRQDILDAIENTNFKVNWGKTRIYNMVRDRGE
WVISRQRVWGVPLPVFYAENGEIIMTKETVNHVADLFAEHGSNIWFEREA
KDLLPEGFTHPGSPNGTFTKETDIMDVWFDSGSSHRGVLETRPELSFPAD
MYLEGSDQYRGWFNSSITTSVATRGVSPYKFLLSHGFVMDGEGKKMSKSL
GNVIVPDQVVKQKGADIARLWVSSTDYLADVRISDEILKQTSDDYRKIRN
TLRFMLGNINDFNPDTDSIPESELLEVDRYLLNRLREFTASTINNYENFD
YLNIYQEVQNFINVELSNFYLDYGKDILYIEQRDSHIRRSMQTVLYQILV
DMTKLLAPILVHTAEEVWSHTPHVKEESVHLADMPKVVEVDQALLDKWRT
FMNLRDDVNRALETARNEKVIGKSLEAKVTIASNDKFNASEFLTSFDALH
QLFIVSQVKVVDKLDDQATAYEHGDIVIEHADGEKCERCWNYSEDLGAVD
ELTHLCPRCQQVVKSLV

3D structure

• PDB: 1ffy Insights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin.
• Chain: A
• Resolution: 2.2 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): S186 S189 D397 T400 W528 K595 K598
• Catalytic site (residue number reindexed from 1): S186 S189 D397 T400 W528 K595 K598
• Enzyme Commision number: 6.1.1.5: isoleucine--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	A	E4 L7 M9 M16 R17 D333 W436 R440 N443 S556 D557 R560 F587 M589 G593 K595 S624 T625 D626 D630 R632 E636 Q640 K647 N650 R653 F654 L702 Q706 Q709 N710 N713 S717 N718 D722 K725 Y729 E813 R816 G822 K823 R888 W890	E4 L7 M9 M16 R17 D333 W436 R440 N443 S556 D557 R560 F587 M589 G593 K595 S624 T625 D626 D630 R632 E636 Q640 K647 N650 R653 F654 L702 Q706 Q709 N710 N713 S717 N718 D722 K725 Y729 E813 R816 G822 K823 R888 W890
BS02	ZN	A	C886 C889 C906 C909	C886 C889 C906 C909
BS03	MRC	A	P56 P57 H64 G66 E554 G555 D557 Q558 H585 F587 V588 S597	P56 P57 H64 G66 E554 G555 D557 Q558 H585 F587 V588 S597	BindingDB: IC50=20000nM

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0000166 nucleotide binding
• GO:0002161 aminoacyl-tRNA editing activity
• GO:0004812 aminoacyl-tRNA ligase activity
• GO:0004822 isoleucine-tRNA ligase activity
• GO:0005524 ATP binding
• GO:0008270 zinc ion binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006412 translation
• GO:0006418 tRNA aminoacylation for protein translation
• GO:0006428 isoleucyl-tRNA aminoacylation
• GO:0106074 aminoacyl-tRNA metabolism involved in translational fidelity

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:1ffy, PDBe:1ffy, PDBj:1ffy
• PDBsum: 1ffy
• PubMed: 10446055
• UniProt: P41972|SYI1_STAAU Isoleucine--tRNA ligase (Gene Name=ileS)