Structure of PDB 6d1v Chain B

Receptor sequence
>6d1vB (length=159) Species: 83333 (Escherichia coli K-12) [Search protein sequence]
SMIDDDGYRPNVGIVICNRQGQVMWARRFGQHSWQFPQGGINPGESAEQA
MYRELFEEVGLSRKDVRILASTRNWLRYKLPKRLVRWDTKPVCIGQKQKW
FLLQLVSGDAEINMQTSSTPEFDGWRWVSYWYPVRQVVSFKRDVYRRVMK
EFASVVMSL
3D structure
PDB6d1v Structural and kinetic insights into stimulation of RppH-dependent RNA degradation by the metabolic enzyme DapF.
ChainB
Resolution1.81 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 3.6.1.-
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 rna B R8 R27 Q34 Q37 G38 G39 E53 Y77 L79 L83 Q95 E120 V137 F139 K140 R9 R28 Q35 Q38 G39 G40 E54 Y78 L80 L84 Q96 E121 V138 F140 K141
BS02 MG B E53 E56 E57 E120 E54 E57 E58 E121
BS03 MG B Q37 E57 E120 Q38 E58 E121
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0005515 protein binding
GO:0016462 pyrophosphatase activity
GO:0016787 hydrolase activity
GO:0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
GO:0034353 mRNA 5'-diphosphatase activity
GO:0110153 RNA NAD-cap (NMN-forming) hydrolase activity
Biological Process
GO:0006402 mRNA catabolic process
GO:0008033 tRNA processing
GO:0050779 RNA destabilization
GO:0110154 RNA decapping
GO:0110155 NAD-cap decapping
Cellular Component
GO:0005737 cytoplasm

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Cellular Component
External links
PDB RCSB:6d1v, PDBe:6d1v, PDBj:6d1v
PDBsum6d1v
PubMed29733359
UniProtP0A776|RPPH_ECOLI RNA pyrophosphohydrolase (Gene Name=rppH)

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