Structure of PDB 4b5m Chain B

Receptor sequence

>4b5mB (length=259) Species: 487 (Neisseria meningitidis)

MLKIISANVNGIRSAYKKGFYEYIAASGADIVCVQELKAQEADLSADMKN
PHGMHGHWHCAEKRGYSGVAVYSKRKPDNVQIGMGIEEFDREGRFVRCDF
GRLSVISLYLPSGSSAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDW
NIAHQNIDLKNWKGNQKNSGFLPEEREWIGKVIHKLGWTDMWRTLYPDVP
GYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVYKDEKFSDHAPL
VVEYDYAAE

3D structure

• PDB: 4b5m Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis.
• Chain: B
• Resolution: 2.758 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): N8 N10 E36 Y109 D149 N151 D221 D246 H247
• Catalytic site (residue number reindexed from 1): N8 N10 E36 Y109 D149 N151 D221 D246 H247
• Enzyme Commision number: 3.1.11.2: exodeoxyribonuclease III.

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	S112 S114 N151 N168 W204 R208 Q210 A211 K214 V216 W218 H247	S112 S114 N151 N168 W204 R208 Q210 A211 K214 V216 W218 H247
BS02	dna	B	Y66 S112 S115 R119	Y66 S112 S115 R119
BS03	dna	B	N10 G11 R13 S14 K38 R64 K167 R208	N10 G11 R13 S14 K38 R64 K167 R208

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003824 catalytic activity
• GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
• GO:0004518 nuclease activity
• GO:0004519 endonuclease activity
• GO:0008081 phosphoric diester hydrolase activity
• GO:0008311 double-stranded DNA 3'-5' DNA exonuclease activity
• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006281 DNA repair
• GO:0006284 base-excision repair

External links

• PDB: RCSB:4b5m, PDBe:4b5m, PDBj:4b5m
• PDBsum: 4b5m
• PubMed: 23035246
• UniProt: Q7DD47