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- PDB-1xsc: Structure of the nudix enzyme AP4A hydrolase from homo sapiens (E... -

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Basic information

Entry
Database: PDB / ID: 1xsc
TitleStructure of the nudix enzyme AP4A hydrolase from homo sapiens (E63A mutant) in complex with ATP
ComponentsBis(5'-nucleosyl)-tetraphosphatase
KeywordsHYDROLASE / nudix enzyme / human AP4A ATP hydrolase / alpha-beta
Function / homology
Function and homology information


bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) / bis(5'-nucleosyl)-tetraphosphatase (symmetrical) activity / AMP biosynthetic process / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / ATP biosynthetic process / nucleobase-containing compound metabolic process / Detoxification of Reactive Oxygen Species / cellular response to oxidative stress / mitochondrial matrix / apoptotic process / GTP binding
Similarity search - Function
Bis(5'-nucleosyl)-tetraphosphatase / : / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...Bis(5'-nucleosyl)-tetraphosphatase / : / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / CNS from a starting structure with ATP 20A from binding site, Refine against NOE, CACB no RAMA potential
AuthorsSwarbrick, J.D. / Buyya, S. / Gunawardana, D. / Gayler, K.R. / McLennan, A.G. / Gooley, P.R.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structure and Substrate-binding Mechanism of Human Ap4A Hydrolase
Authors: Swarbrick, J.D. / Buyya, S. / Gunawardana, D. / Gayler, K.R. / McLennan, A.G. / Gooley, P.R.
History
DepositionOct 18, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bis(5'-nucleosyl)-tetraphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8252
Polymers17,3181
Non-polymers5071
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Bis(5'-nucleosyl)-tetraphosphatase / Diadenosine 5' / 5'''-P1 / P4-tetraphosphate asymmetrical hydrolase / Diadenosine tetraphosphatase ...Diadenosine 5' / 5'''-P1 / P4-tetraphosphate asymmetrical hydrolase / Diadenosine tetraphosphatase / Ap4A hydrolase / Ap4AASE


Mass: 17317.809 Da / Num. of mol.: 1 / Mutation: E63A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6-P3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P50583, bis(5'-nucleosyl)-tetraphosphatase (asymmetrical)
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
12213C NOESY over Aromatic/Anomeric
NMR detailsText: This calcualtion includes ATP constraints. Slow cooling, Lower temperature (20000K rather than 50000K) ATP starts 20A from lowest energy conformer Residues 1 and 2 are changed from GP to ...Text: This calcualtion includes ATP constraints. Slow cooling, Lower temperature (20000K rather than 50000K) ATP starts 20A from lowest energy conformer Residues 1 and 2 are changed from GP to Alanine in the calculations. These are from the non native precission cleavage site and are unstructrued.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0mM human AP4A hydrolase, 13C 15N ATP20mM MgCl2, 20mM imidazole, pH 6.5, 90% H2O 10% D2O, 10mM DTT, 1mM EDTA, 1.5mM ATP (13C,15N labelled)
21.0mM human AP4A hydrolase, 13C 15N ATP20mM MgCl2, 20mM imidazole, pH 6.5, 100% D2O, 10mM DTT, 1mM EDTA, 1.5mM ATP (13C, 15N labelled)
Sample conditionsIonic strength: 51mM / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR softwareName: CNS / Version: 1 / Classification: refinement
RefinementMethod: CNS from a starting structure with ATP 20A from binding site, Refine against NOE, CACB no RAMA potential
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 25

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