Structure of PDB 2xzl Chain A

Receptor sequence

>2xzlA (length=756) Species: 4932 (Saccharomyces cerevisiae)

NSCAYCGIDSAKCVIKCNSCKKWFCNTKNGTSSSHIVNHLVLSHHNVVSL
HPDSDLGDTVLECYNCGRKNVFLLGFVSVVLLCRIPCAQTKWDTDQWQPL
IEDRQLLSWVAEQPTEEEKLKARLITPSQISKLEAKWRSNKDATIPPLLL
RYQDAYEYQRSYGPLIKLEADYDKQLKESQEHISVSWSLALNNRHLASFT
KVAIGDEMILWYSGMQHPDWEGRGYIVRLPNDTFTLELKPSKTPPPTHLT
TGFTAEFIWKGTSYDRMQDALKKFAIDKKSISGYLYYKILGHQVVDISFD
VPLPKEFSIPNFAQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIV
YHLSKIHKDRILVCAPSNVAVDHLAAKLRDLGLKVVRLTAKSREDVESSV
SNLALHNLVGRGAKGELKNLLKLKDEVGELSASDTKRFVKLVRKTEAEIL
NKADVVCCTCVGAGDKRLDTKFRTVLIDESTQASEPECLIPIVKGAKQVI
LVGDHQQLGPVILERKAADAGLKQSLFERLISLGHVPIRLEVQYRMNPYL
SEFPSNMFYEGSLQNGVTIEQRTVPNSKFPWPIRGIPMMFWANYGREEIS
ANGTSFLNRIEAMNCERIITKLFRDGVKPEQIGVITPYEGQRAYILQYMQ
MNGSLDKDLYIKVEVASVDAFQGREKDYIILSCVRANEQQAIGFLRDPRR
LNVGLTRAKYGLVILGNPRSLARNTLWNHLLIHFREKGCLVEGTLDNLQL
CTVQLV

3D structure

• PDB: 2xzl Molecular Mechanisms for the RNA-Dependent ATPase Activity of Upf1 and its Regulation by Upf2.
• Chain: A
• Resolution: 2.4 Å

Enzymatic activity

• Enzyme Commision number: 3.6.4.12: DNA helicase.
  3.6.4.13: RNA helicase.

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	D297 E298 Y316 K354 T356 S357 P460 N462 A484 K485 S486 T553 V555 V605 L607 T698 S699 Y732 E733 S761 D763 G787 F788	D206 E207 Y225 K260 T262 S263 P366 N368 A390 K391 S392 T459 V461 V511 L513 T604 S605 Y638 E639 S667 D669 G693 F694	PDBbind-CN: Kd=202nM
BS02	ZN	A	C62 C84 H94	C3 C25 H35
BS03	ZN	A	C76 H98 H104	C17 H39 H45
BS04	ZN	A	C122 C125 C148	C63 C66 C83
BS05	ADP	A	Q408 Q413 G433 T434 G435 K436 T437 V438 Y638 R639 E769	Q314 Q319 G339 T340 G341 K342 T343 V344 Y544 R545 E675
BS06	ALF	A	P432 G433 K436 Q601 R639 G767 R801	P338 G339 K342 Q507 R545 G673 R707

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003724 RNA helicase activity
• GO:0004386 helicase activity
• GO:0005524 ATP binding
• GO:0008270 zinc ion binding
• GO:0016887 ATP hydrolysis activity

Biological Process

• GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:2xzl, PDBe:2xzl, PDBj:2xzl
• PDBsum: 2xzl
• PubMed: 21419344
• UniProt: P30771|RENT1_YEAST ATP-dependent helicase NAM7 (Gene Name=NAM7)