Structure of PDB 4kpy Chain B

Receptor sequence

>4kpyB (length=675) Species: 262724 (Thermus thermophilus HB27) [Search protein sequence]

HLGKTEVFLNRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVARR
AGGVTVRMGDGLASWSPPEVLVLEGTLARMGQTYAYRLYPKGRRPLDPKD
PGERSVLSALARRLLQERLRRLEGVWVEGLAVYRREHARGPGWRVLGGAV
LDLWVSDSGAFLLEVDPAYRILCEMSLEAWLAQGHPLPKRVRNAYDRRTW
ELLRLGEEDPKELPGGLSLLDYHASKGRLQGREGGRVAWVADPKPIPHLT
GLLVPVLTLEDLHEEELALSLPWEERRRRTREIASWIGRRLGLGTPEAVR
AQAYRLSIPKLMGRRAVSKPADALRVGFYRAQETALALLRLDGAQGWPEF
LRRALLRAFGASGASLRLHTLHAHPSQGLAFREALRKAKEEGVQAVLVLT
PPMAWEDRNRLKALLLREGLPSQILNVPLREEERHRWENALLGLLAKAGL
QVVALSGAYPAELAVGFDAGGRESFRFGGAACAVGGDGGHLLWTLPEAQA
GERIPQEVVWDLLEETLWAFRRKAGRLPSRVLLLRDGRVPQDEFALALEA
LAREGIAYDLVSVRKSGGGRVYPVQGRLADGLYVPLEDKTFLLLTVHRDF
RGTPRPLKLVHEAGDTPLEALAHQIFHLTRLYPASGFAFPRLPAPLHLAD
RLVKEVGRLGIRHLKEVDREKLFFV

3D structure

PDB

4kpy Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage.

Chain

Resolution

2.406 Å

3D
structure

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Enzymatic activity

Enzyme Commision number

3.1.24.-

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)
BS01	dna	B	Y43 A170 Y171 R172 I173 R192 T201 V264 L265 L279 S280 L281 R286 M413 W415 K422 Q433 I434 N436 R446 N449 K457 R486 E512 R513 R580 R611 G612 T613 P614 R615 S645 A648 P650 R651 H657 R661 V685	Y41 A168 Y169 R170 I171 R190 T199 V256 L257 L269 S270 L271 R276 M403 W405 K412 Q423 I424 N426 R436 N439 K447 R476 E502 R503 R570 R601 G602 T603 P604 R605 S635 A638 P640 R641 H647 R651 V675
BS02	dna	B	E268 H271 K329 H445 D478 G480 G481 K575 D590 V606 R608 F610 F647 F649 K664	E260 H263 K319 H435 D468 G470 G471 K565 D580 V596 R598 F600 F637 F639 K654
BS03	dna	B	P44 R51 R81 R114 G547 R548 R574 K575 S576 K618	P42 R49 R79 R112 G537 R538 R564 K565 S566 K608
BS04	DT	B	G38 R39	G36 R37
BS05	DT	B	Y197 R200 Y226 H227 R232 P255 H256	Y195 R198 Y222 H223 R228 P247 H248
BS06	MN	B	D478 D546	D468 D536
BS07	MN	B	D478 D660	D468 D650

Gene Ontology

	Molecular Function
GO:0003676	nucleic acid binding
GO:0003677	DNA binding
GO:0003723	RNA binding
GO:0004519	endonuclease activity
GO:0004520	DNA endonuclease activity
GO:0030145	manganese ion binding
GO:0046872	metal ion binding

	Biological Process
GO:0006260	DNA replication
GO:0044355	clearance of foreign intracellular DNA

View graph for
Molecular Function

View graph for
Biological Process

External links

PDB	RCSB:4kpy, PDBe:4kpy, PDBj:4kpy
PDBsum	4kpy
PubMed	24374628
UniProt	Q746M7\|AGO_THET2 Protein argonaute (Gene Name=ago)

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