Structure of PDB 2a8t Chain A

Receptor sequence
>2a8tA (length=192) Species: 8355 (Xenopus laevis) [Search protein sequence]
PRNISREESLQLEGYKHACHALLHAPSQAKLFDRVPIRRVLLMMMRFDGR
LGFPGGFVDTRDISLEEGLKRELEEELGPALATVEVTEDDYRSSQVREHP
QKCVTHFYIKELKLEEIERIEAEAVNAKDHGLEVMGLIRVPLYTLRDRVG
GLPAFLCNNFIGNSKSQLLYALRSLKLLREDQIQEVLKASHR
3D structure
PDB2a8t Crystal structures of U8 snoRNA decapping nudix hydrolase, X29, and its metal and cap complexes
ChainA
Resolution2.1 Å
3D
structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Enzyme Commision number 3.6.1.62: 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase.
3.6.1.64: inosine diphosphate 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 MN A G72 E93 G55 E76
BS02 MN A E89 E93 E150 E72 E76 E133
BS03 MGT A R63 F64 G72 G73 F74 E89 E150 R46 F47 G55 G56 F57 E72 E133
BS04 ADN A H37 F74 T122 I178 N180 S181 Q184 H20 F57 T105 I161 N163 S164 Q167
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0008235 metalloexopeptidase activity
GO:0016787 hydrolase activity
GO:0030145 manganese ion binding
GO:0030515 snoRNA binding
GO:0035870 dITP diphosphatase activity
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0050897 cobalt ion binding
GO:0097383 dIDP phosphatase activity
GO:0110152 RNA NAD+-cap (NAD+-forming) hydrolase activity
GO:0140933 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity
GO:1990003 IDP phosphatase activity
GO:1990174 phosphodiesterase decapping endonuclease activity
Biological Process
GO:0006402 mRNA catabolic process
GO:0009117 nucleotide metabolic process
GO:0016077 sno(s)RNA catabolic process
GO:0035863 dITP catabolic process
GO:0090068 positive regulation of cell cycle process
GO:0110155 NAD-cap decapping
GO:2000233 negative regulation of rRNA processing
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2a8t, PDBe:2a8t, PDBj:2a8t
PDBsum2a8t
PubMed16472752
UniProtQ6TEC1|NUD16_XENLA U8 snoRNA-decapping enzyme (Gene Name=nudt16)

[Back to BioLiP]