BioLiP

Structure of PDB 4nca Chain A

Receptor sequence

>4ncaA (length=683) Species: 274 (Thermus thermophilus) [Search protein sequence]

HLGKTEVFLNRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVARR
AGGVTVRMGDGLASWSPPEVLVLEGTLARMGQTYAYRLYPKGRRPLDPKD
PGERSVLSALARRLLQERLRRLEGVWVEGLAVYRREHARGPGWRVLGGAV
LDLWVSDSGAFLLEVDPAYRILCEMSLEAWLAQGHPLPKRVRNAYDRRTW
ELLRLGEEDPKELPLPGGLSLLDYHASKGRLQGREGGRVAWVADPKDPRK
PIPHLTGLLVPVLTLEDLHEEEGSLALSLPWEERRRRTREIASWIGRRLG
LGTPEAVRAQAYRLSIPKLMGRRAVSKPADALRVGFYRAQETALALLRLD
GAQGWPEFLRRALLRAFGASGASLRLHTLHAHPSQGLAFREALRKAKEEG
VQAVLVLTPPMAWEDRNRLKALLLREGLPSQILNVPLREEERHRWENALL
GLLAKAGLQVVALSGAYPAELAVGFDAGGRESFRFGGAACAVGGDGGHLL
WTLPEAQAGERIPQEVVWDLLEETLWAFRRKAGRLPSRVLLLRDGRVPQD
EFALALEALAREGIAYDLVSVRKSGGGRVYPVQGRLADGLYVPLEDKTFL
LLTVHRDFRGTPRPLKLVHEAGDTPLEALAHQIFHLTRLYPASGFAFPRL
PAPLHLADRLVKEVGRLGIRHLKEVDREKLFFV

3D structure

PDB

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

Chain

Resolution

2.489 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	A	Y43 A170 Y171 R172 I173 R192 T201 V264 L265 L279 S280 L281 R286 M413 W415 R418 K422 Q433 I434 N436 R446 N449 K457 E512 R513 P550 R580 R611 G612 T613 P614 R615 A644 S645 A648 P650 R651 H657 R661 V685	Y41 A168 Y169 R170 I171 R190 T199 V262 L263 L277 S278 L279 R284 M411 W413 R416 K420 Q431 I432 N434 R444 N447 K455 E510 R511 P548 R578 R609 G610 T611 P612 R613 A642 S643 A646 P648 R649 H655 R659 V683
BS02	dna	A	L267 E268 H271 K329 W415 H445 G480 G481 D590 V606 R608 F610 F647 F649 K664 R668	L265 E266 H269 K327 W413 H443 G478 G479 D588 V604 R606 F608 F645 F647 K662 R666
BS03	dna	A	P44 A47 R51 R114 G547 R574 K575 S576	P42 A45 R49 R112 G545 R572 K573 S574
BS04	DT	A	Y197 R200 L217 P218 L223 Y226 H227 R232 P255 H256	Y195 R198 L215 P216 L221 Y224 H225 R230 P253 H254
BS05	MG	A	D478 D546	D476 D544
BS06	DT	A	G38 R39	G36 R37
BS07	MG	A	D478 D660	D476 D658

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

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