5W6X | pdb_00005w6x

Crystal structure of the HsNUDT16 in complex with Mg+2 and ADP-ribose

• PDB DOI: https://doi.org/10.2210/pdb5W6X/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-06-18 Released: 2018-12-19 
• Deposition Author(s): Thirawatananond, P., Gabelli, S.B.
• Funding Organization(s): Allegheny Health Network, DoD-CDMRP

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.238 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

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., Nathan, S., Lambrecht, M.J., Brichacek, M., Hergenrother, P.J., Leung, A.K.L., Gabelli, S.B.

(2019) Sci Rep 9: 5940-5940

• PubMed: 30976021 
• DOI: https://doi.org/10.1038/s41598-019-39491-w
• Primary Citation Related Structures: 
  5VY2, 5W6X, 5W6Z, 5WJI, 6B09


• PubMed Abstract: 
  

  ADP-ribosylation is a post-translational modification that occurs on chemically diverse amino acids, including aspartate, glutamate, lysine, arginine, serine and cysteine on proteins and is mediated by ADP-ribosyltransferases, including a subset commonly known as poly(ADP-ribose) polymerases. ADP-ribose can be conjugated to proteins singly as a monomer or in polymeric chains as poly(ADP-ribose). While ADP-ribosylation can be reversed by ADP-ribosylhydrolases, this protein modification can also be processed to phosphoribosylation by enzymes possessing phosphodiesterase activity, such as snake venom phosphodiesterase, mammalian ectonucleotide pyrophosphatase/phosphodiesterase 1, Escherichia coli RppH, Legionella pneumophila Sde and Homo sapiens NudT16 (HsNudT16). Our studies here sought to utilize X-ray crystallographic structures of HsNudT16 in complex with monomeric and dimeric ADP-ribose in identifying the active site for binding and processing free and protein-conjugated ADP-ribose into phosphoribose forms. These structural data guide rational design of mutants that widen the active site to better accommodate protein-conjugated ADP-ribose. We identified that several HsNudT16 mutants (Δ17, F36A, and F61S) have reduced activity for free ADP-ribose, similar processing ability against protein-conjugated mono(ADP-ribose), but improved catalytic efficiency for protein-conjugated poly(ADP-ribose). These HsNudT16 variants may, therefore, provide a novel tool to investigate different forms of ADP-ribose.

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Organizational Affiliation: 
• Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA.
Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
Department of Chemistry, University of Illinois, Urbana, IL, 61801, USA.
Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA. [e-mail].
Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA. [e-mail].
Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. [e-mail].
Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. [e-mail].
Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA. [e-mail].
Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, SAXS

Macromolecule Content 

• Total Structure Weight: 44.1 kDa 
• Atom Count: 3,141 
• Modeled Residue Count: 353 
• Deposited Residue Count: 390 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
U8 snoRNA-decapping enzyme	A, B	195	Homo sapiens	Mutation(s): 1  Gene Names: NUDT16 EC: 3.6.1.62 (PDB Primary Data), 3.6.1.64 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96DE0 (Homo sapiens) Explore Q96DE0  Go to UniProtKB:  Q96DE0
PHAROS:  Q96DE0 GTEx:  ENSG00000198585

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
APR	C [auth A], G [auth B]	ADENOSINE-5-DIPHOSPHORIBOSE C15 H23 N5 O14 P2 SRNWOUGRCWSEMX-KEOHHSTQSA-N
PEG	K [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ACY	F [auth A], J [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
MG	D [auth A], E [auth A], H [auth B], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.238 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.755	α = 90
b = 46.319	β = 107.65
c = 74.238	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data collection
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
Coot	model building
AMoRE	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-12-19 
Deposition Author(s): Thirawatananond, P., Gabelli, S.B.

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Funding Organization	Location	Grant Number
Allegheny Health Network	United States	--
DoD-CDMRP	United States	--

Revision History  

• Version 1.0: 2018-12-19
  Type: Initial release
  
• Version 1.1: 2019-06-05
  Changes: Data collection, Database references
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-04-03
  Changes: Refinement description