Structure of PDB 5xd5 Chain B

Receptor sequence

>5xd5B (length=289) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

HTVRAAGAVLWRDATVEVAVIHRPRYDDWSLPKGKLDQGETEPVAAAREI
HEETGHTAVLGRRLGRVTYPIPQGTKRVWYWAAKSTGGDFSPNDEVDKLV
WLPVDAAMDQLQYPDDRKVLRRFVKRPVDTKTVLVVRHGTAGRRSRYKGD
DRKRPLDKRGRAQAEALVAQLMAFGATTLYAADRVRCHQTIEPLAQELDQ
LIHNEPLLTEEAYAADHKAARKRLLEIAGRPGNPVICTQGKVIPGLIEWW
CERAKVRPETTGNRKGSTWVLSLSDGELVGADYLSPPDE

3D structure

• PDB: 5xd5 Hydrolysis of diadenosine polyphosphates. Exploration of an additional role of Mycobacterium smegmatis MutT1
• Chain: B
• Resolution: 1.75 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): T23 A29
• Catalytic site (residue number reindexed from 1): T2 A8
• Enzyme Commision number: 3.6.1.58: 8-oxo-dGDP phosphatase.
  3.6.1.61: diadenosine hexaphosphate hydrolase (ATP-forming).
  3.6.1.69: 8-oxo-(d)GTP phosphatase.

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	ATP	B	R55 R57 Y58 K65 K67 Y101 I103 K108 Y145	R23 R25 Y26 K33 K35 Y69 I71 K76 Y113
BS02	PO4	B	R57 K67	R25 K35
BS03	MG	B	K65 E85 E127	K33 E53 E95
BS04	MG	B	E81 E85 E127	E49 E53 E95
BS05	F	B	E81 E127	E49 E95

Gene Ontology

Molecular Function

• GO:0008413 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity
• GO:0016787 hydrolase activity
• GO:0044715 8-oxo-dGDP phosphatase activity
• GO:0044716 8-oxo-GDP phosphatase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006260 DNA replication
• GO:0006281 DNA repair

External links

• PDB: RCSB:5xd5, PDBe:5xd5, PDBj:5xd5
• PDBsum: 5xd5
• PubMed: 28705712
• UniProt: A0QUZ2|MUTT1_MYCS2 8-oxo-(d)GTP phosphatase (Gene Name=mutT1)