Structure of PDB 5k77 Chain B

Receptor sequence

>5k77B (length=349) Species: 5759 (Entamoeba histolytica)

QIQHIAIVGCVHGKYREMYRQLSEYEKSTGKEISFVICTGDMQTLRYEAD
LVYLKVPPKYKQMGDFHLYYEGKEKAPYLTLFIGGNAESSNVLLHLYNGG
FVCFNMYYLGVCSCININGLRIVGVSGIYKSFDEKKPYTYPPSPNDVVSL
FHTRNYVIQMLSNLSQSSQIDISLSHDWPQGIVMKGNYKQLYRFQPGFKK
DGASLGSPINKVILNTLKPKYWISGHMHCEYHAEEGPTHFIALGKIGYKN
AISYLDLPLKQKTDLEYDKDWVCNLIMTWPAFSNKAQFPDLSYSISELLS
KRTKELDKKIIELWEKYIGLKIIYDSDTFDIQFTSRRFYIEKIYNELNI

3D structure

• PDB: 5k77 Metal dependence and branched RNA cocrystal structures of the RNA lariat debranching enzyme Dbr1.
• Chain: B
• Resolution: 2.17 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	B	H16 Q47 V60 K63 Y64 I132 K134 F136 F155 H156 K249	H12 Q43 V56 K59 Y60 I128 K130 F132 F151 H152 K245
BS02	rna	B	H16 N90 D205 L209 H230 M231 H232	H12 N86 D201 L205 H226 M227 H228
BS03	FE2	B	D45 N90 H180 H230	D41 N86 H176 H226
BS04	ZN	B	C14 H16 H232	C10 H12 H228
BS05	OH	B	H180 H230	H176 H226

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:5k77, PDBe:5k77, PDBj:5k77
• PDBsum: 5k77
• PubMed: 27930312
• UniProt: C4M1P9|DBR1_ENTH1 Lariat debranching enzyme (Gene Name=DBR1)