Structure of PDB 5xd4 Chain A

Receptor sequence

>5xd4A (length=293) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

KHTVRAAGAVLWRDAPATVEVAVIHRPRYDDWSLPKGKLDQGETEPVAAA
REIHEETGHTAVLGRRLGRVTYPIPQGTKRVWYWAAKSTGGDFSPNDEVD
KLVWLPVDAAMDQLQYPDDRKVLRRFVKRPVDTKTVLVVRHGTAGRRSRY
KGDDRKRPLDKRGRAQAEALVAQLMAFGATTLYAADRVRCHQTIEPLAQE
LDQLIHNEPLLTEEAYAADHKAARKRLLEIAGRPGNPVICTQGKVIPGLI
EWWCERAKVRPETTGNRKGSTWVLSLSDGELVGADYLSPPDEK

3D structure

• PDB: 5xd4 Hydrolysis of diadenosine polyphosphates. Exploration of an additional role of Mycobacterium smegmatis MutT1
• Chain: A
• Resolution: 1.47 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): T23 A29
• Catalytic site (residue number reindexed from 1): T3 A9
• 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	A	R55 Y58 K65 K67 Y101 K108 Y145	R26 Y29 K36 K38 Y72 K79 Y116
BS02	ATP	A	R169 H170 R175 R176 Y179 G181 R186 R218 Q271 G272 K273 K297	R140 H141 R146 R147 Y150 G152 R157 R189 Q242 G243 K244 K268
BS03	MG	A	K65 E85	K36 E56

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:5xd4, PDBe:5xd4, PDBj:5xd4
• PDBsum: 5xd4
• PubMed: 28705712
• UniProt: A0QUZ2|MUTT1_MYCS2 8-oxo-(d)GTP phosphatase (Gene Name=mutT1)