Structure of PDB 8edj Chain A

Receptor sequence

>8edjA (length=373) Species: 9544 (Macaca mulatta)

QIRNMVEPMDPRTFVSNFNNRPILSGLDTVWLCCEVKTKDPSGPPLDAKI
FQGKVYPKAKYHPEMRFLRWFHKWRQLHHDQEYKVTWYVSWSPCTRCANS
VATFLAKDPKVTLTIFVARLYYFWKPDYQQALRILAEAGATMKIMNYNEF
QDCWNKFVDGRGKPFKPWNNLPKHYTLLQATLGELLRHLMDPGTFTSNFN
NKPWVSGQHETYLCYKVERLHNDTWVPLNQHRGFLRNQAPNIHGFPKGRH
AALCFLDLIPFWKLDGQQYRVTCFTSWSPCFSCAQEMAKFISNNEHVSLC
IFAARIYDDQGRYQEGLRTLHRDGAKIAMMNYSEFEYCWDTFVDRQGRPF
QPWDGLDEHSQALSGRLRAILQN

3D structure

• PDB: 8edj Structural basis of sequence-specific RNA recognition by the antiviral factor APOBEC3G.
• Chain: A
• Resolution: 1.83 Å

Enzymatic activity

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

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	R24 I26 L27 S28 V58 Y59 P60 A62 H65 W94 R99 Y124 Y125 F126 W127 Y131 F268 K270	R21 I23 L24 S25 V55 Y56 P57 A59 H62 W91 R96 Y121 Y122 F123 W124 Y128 F261 K263
BS02	ZN	A	H65 C97 C100	H62 C94 C97
BS03	ZN	A	H257 C287 C290	H250 C280 C283

Gene Ontology

Molecular Function

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

Biological Process

• GO:0009972 cytidine deamination
• GO:0010526 retrotransposon silencing
• GO:0016554 cytidine to uridine editing
• 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:0005737 cytoplasm
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8edj, PDBe:8edj, PDBj:8edj
• PDBsum: 8edj
• PubMed: 36470880
• UniProt: Q7YR23|ABC3G_MACMU DNA dC->dU-editing enzyme APOBEC-3G (Gene Name=APOBEC3G)