Structure of PDB 5sww Chain A Binding Site BS01

Receptor Information

>5sww Chain A (length=183) Species: 9606 (Homo sapiens)

RHLMDPHIFTSNFNNGIGRHKTYLCYEVERLDSVKMDQHRGFLHNQAKNL
LCGFYGRHAALRFLDLVPSLQLDPAQIYRVTWFISWSPCFSWGCAGEVRA
FLQENTHVRLRIFAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFKHCW
DTFVDHQGCPFQPWDGLDEHSQALSGRLRAILQ

Ligand information

>5sww Chain E (length=6)

atcggg

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5sww Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B.
• Resolution: 3.151 Å
• Binding residue (original residue number in PDB): R28 H29 K30 T31 N57 A59 K60 H70 W98 S99 Y130 D131 Y132
• Binding residue (residue number reindexed from 1): R19 H20 K21 T22 N45 A47 K48 H58 W86 S87 Y118 D119 Y120

Enzymatic activity

• Enzyme Commision number: 3.5.4.38: single-stranded DNA cytosine deaminase.

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003824 catalytic activity
• GO:0004126 cytidine deaminase activity
• GO:0005515 protein binding
• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0010526 retrotransposon silencing
• GO:0016554 cytidine to uridine editing
• GO:0044029 positive regulation of gene expression via chromosomal CpG island demethylation
• GO:0044355 clearance of foreign intracellular DNA
• GO:0045071 negative regulation of viral genome replication
• GO:0045087 innate immune response
• GO:0045869 negative regulation of single stranded viral RNA replication via double stranded DNA intermediate
• GO:0051607 defense response to virus
• GO:0070383 DNA cytosine deamination

Cellular Component

• GO:0000932 P-body
• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005737 cytoplasm

External links

• PDB: RCSB:5sww, PDBe:5sww, PDBj:5sww
• PDBsum: 5sww
• PubMed: 27991903
• UniProt: P31941|ABC3A_HUMAN DNA dC->dU-editing enzyme APOBEC-3A (Gene Name=APOBEC3A)