Brand  (β version)

PDB ID: 6B09

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Ligands
Code Name Style Show Link
C7G [(2~{R},3~{S},4~{S},5~{S})-5-(6-aminopurin-9-yl)-4-[(2~{S},3~{S},4~{S},5~{S})-5-[[[[(2~{R},3~{R},4~{S},5~{S})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methyl phosphono hydrogen phosphate PoSSuM
CL Chloride ion PoSSuM
MG Magnesium ion PoSSuM
NA Sodium ion PoSSuM
Non-standard Residues
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Structure summary

Code : 6B09   PDBj   RCSB PDB   PDBe
Header : HYDROLASE
Title : Crystal structure of HsNUDT16 in complex with diADPR (soaked)
Release Data : 2019-01-09
Compound :
mol_id molecule chains synonym
1 U8 snoRNA-decapping enzyme A,B IDP phosphatase,IDPase,Inosine diphosphate phosphatase,Nucleoside diphosphate-linked moiety X motif 16,Nudix motif 16,Nudix hydrolase 16,U8 snoRNA-binding protein H29K,m7GpppN-mRNA hydrolase
ec: 3.6.1.62,3.6.1.64
mutation: A22V
Source :
mol_id organism_scientific organism_common expression_system
1 Homo sapiens  (taxid:9606) Human Escherichia coli  (taxid:562)
gene: NUDT16
expression_system_strain: BL21(DE3) codon plus RIPL
expression_system_vector_type: plasmid
expression_system_plasmid: pNIC28-Bsa4
Authors : Thirawatananond, P., Gabelli, S.B.
Keywords : nudix hydrolase, decapping enzyme, demodification of parylation, hydrolase
Exp. method : X-RAY DIFFRACTION ( 3.2000 Å )
Citation :

Structural analyses of NudT16-ADP-ribose complexes direct rational design of mutants with improved processing of poly(ADP-ribosyl)ated proteins.

Thirawatananond, P.,McPherson, R.L.,Malhi, J.  et al.
(2019)  Sci Rep  9 : 5940 - 5940

PubMed: 30976021
DOI: 10.1038/s41598-019-39491-w

Reaction

Chain : A, B
UniProt : Q96DE0 (NUD16_HUMAN)
Reaction: EC: Evidence:
Physiological Direction:
a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + H2O = a 5'-end phospho-ribonucleoside in mRNA + 2 H(+) + N(7)-methyl-GDP 3.6.1.62 PubMed:15053875, PubMed:17567574, PubMed:18820299, PubMed:21070968, PubMed:21337011
left-to-right PubMed:15053875, PubMed:17567574, PubMed:18820299, PubMed:21070968, PubMed:21337011
H2O + IDP = H(+) + IMP + phosphate 3.6.1.64 PubMed:20385596, PubMed:26121039
left-to-right
dIDP + H2O = dIMP + H(+) + phosphate 3.6.1.64 PubMed:20385596, PubMed:26121039
left-to-right
a 5'-end NAD(+)-phospho-ribonucleoside in mRNA + H2O = a 5'- end phospho-adenosine-phospho-ribonucleoside in mRNA + beta- nicotinamide D-ribonucleotide + 2 H(+) - PubMed:32432673
left-to-right
a 5'-end FAD-phospho-ribonucleoside in mRNA + H2O = a 5'-end phospho-adenosine-phospho-ribonucleoside in mRNA + FMN + 2 H(+) - PubMed:32432673
left-to-right
a 5'-end CoA-ribonucleoside in mRNA + H2O = (R)-4'- phosphopantetheine + a 5'-end phospho-adenosine-phospho- ribonucleoside in mRNA + 2 H(+) - UniProtKB:Q6P3D0
left-to-right