Structure of PDB 8dzk Chain A

Receptor sequence

>8dzkA (length=349) Species: 5759 (Entamoeba histolytica)

QIQHIAIVGCVHGKYREMYRQLSEYEKSTGKEISFVICTGDMQTLRYEAD
LVYLKVPPKYKQMGDFHLYYEGKEKAPYLTLFIGGNHESSNVLLHLYNGG
FVCFNMYYLGVCSCININGLRIVGVSGIYKSFDEKKPYTYPPSPNDVVSL
FHTRNYVIQMLSNLSQSSQIDISLSHDWPQGIVMKGNYKQLYRFQPGFKK
DGASLGSPINKVILNTLKPKYWISGHMHCEYHAEEGPTHFIALGKIGYKN
AISYLDLPLKQKTDLEYDKDWVCNLIMTWPAFSNKAQFPDLSYSISELLS
KRTKELDKKIIELWEKYIGLKIIYDSDTFDIQFTSRRFYIEKIYNELNI

3D structure

• PDB: 8dzk Crystal Structure of the RNA Lariat Debranching Enzyme Dbr1 with Hydrolyzed Phosphorothioate RNA Product.
• Chain: A
• Resolution: 2.1 Å

Enzymatic activity

• Enzyme Commision number: 3.1.4.-

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	H16 D45 K59 Y64 N90 H91 K134 F155 H156 G201 D205 H230 M231 H232 K249	H12 D41 K55 Y60 N86 H87 K130 F151 H152 G197 D201 H226 M227 H228 K245
BS02	FE2	A	D45 N90 H180 H230	D41 N86 H176 H226
BS03	ZN	A	C14 H16 H232	C10 H12 H228

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0005506 iron ion binding
• GO:0008270 zinc ion binding
• GO:0008419 RNA lariat debranching enzyme activity
• GO:0016787 hydrolase activity
• GO:0030145 manganese ion binding
• GO:0046872 metal ion binding

Biological Process

• GO:0000375 RNA splicing, via transesterification reactions
• GO:0000398 mRNA splicing, via spliceosome
• GO:0006397 mRNA processing

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0048471 perinuclear region of cytoplasm

External links

• PDB: RCSB:8dzk, PDBe:8dzk, PDBj:8dzk
• PDBsum: 8dzk
• PubMed: 36484984
• UniProt: C4M1P9|DBR1_ENTH1 Lariat debranching enzyme (Gene Name=DBR1)