Structure of PDB 5nnu Chain A

Receptor sequence

>5nnuA (length=231) Species: 37296 (Human gammaherpesvirus 8)

DDRDLLLAPKWISFLSLSSFLKQKLLSLLRQIRELRLTTTVYPPQDKLMW
WSHCCDPEDIKVVILGQDPYHKGQATGLAFSVDPQCQVPPSLRSIFRELE
ASVPNFSTPSHGCLDSWARQGVLLLNTVLTVEKGSHELGWDWFTSFIISS
ISSKLEHCVFLLWGRKAIDRTPLINAQKHLVLTAQHPSPLASLGGRHSRW
PRFQGCNHFNLANDYLTRHRRETVDWGLLEQ

3D structure

• PDB: 5nnu A structurally conserved motif in gamma-herpesvirus uracil-DNA glycosylases elicits duplex nucleotide-flipping.
• Chain: A
• Resolution: 2.97 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D91 Y93 F103 H213
• Catalytic site (residue number reindexed from 1): D68 Y70 F80 H186
• Enzyme Commision number: 3.2.2.27: uracil-DNA glycosylase.

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	dna	A	Q90 D91 P113 S114 G191 R192 Q212 H213 S215 P216 L217 A218 G221 G222 S225	Q67 D68 P90 S91 G164 R165 Q185 H186 S188 P189 L190 A191 G194 G195 S198
BS02	dna	A	R116 R120 P216 S219 L220 R223	R93 R97 P189 S192 L193 R196
BS03	dna	A	S39 F173 S180 K181	S16 F146 S153 K154
BS04	dna	A	F43 L44	F20 L21

Gene Ontology

Molecular Function

• GO:0004844 uracil DNA N-glycosylase activity
• GO:0016787 hydrolase activity
• GO:0016799 hydrolase activity, hydrolyzing N-glycosyl compounds

Biological Process

• GO:0006281 DNA repair
• GO:0006284 base-excision repair
• GO:0097510 base-excision repair, AP site formation via deaminated base removal

Cellular Component

• GO:0042025 host cell nucleus

External links

• PDB: RCSB:5nnu, PDBe:5nnu, PDBj:5nnu
• PDBsum: 5nnu
• PubMed: 29596604
• UniProt: F5HFA1|UNG_HHV8P Uracil-DNA glycosylase (Gene Name=ORF46)