Structure of PDB 5nnu Chain B

Receptor sequence

>5nnuB (length=230) Species: 37296 (Human gammaherpesvirus 8)

DLLLAPKWISFLSLSSFLKQKLLSLLRQIRELRLTTTVYPPQDKLMWWSH
CCDPEDIKVVILGQDPYHKGQATGLAFSVDPQCQVPPSLRSIFRELEASV
PNFSTPSHGCLDSWARQGVLLLNTVLTVEKGRASHELGWDWFTSFIISSI
SSKLEHCVFLLWGRKAIDRTPLINAQKHLVLTAQHPSPLASLGGRHSRWP
RFQGCNHFNLANDYLTRHRRETVDWGLLEQ

3D structure

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

Enzymatic activity

• Catalytic site (original residue number in PDB): D91 Y93 F103 H213
• Catalytic site (residue number reindexed from 1): D65 Y67 F77 H185
• 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	B	Q90 D91 P113 S114 G191 R192 Q212 H213 S215 P216 L217 A218 G221 G222 S225	Q64 D65 P87 S88 G163 R164 Q184 H185 S187 P188 L189 A190 G193 G194 S197
BS02	dna	B	R116 R120 P216 S219 L220 R223	R90 R94 P188 S191 L192 R195
BS03	dna	B	S39 F173 S180 K181	S13 F145 S152 K153
BS04	dna	B	F43 L44 K47	F17 L18 K21

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)