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- PDB-3gc6: Structural insights into the catalytic mechanism of CD38: Evidenc... -

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Basic information

Entry
Database: PDB / ID: 3gc6
TitleStructural insights into the catalytic mechanism of CD38: Evidence for a conformationally flexible covalent enzyme-substrate complex.
ComponentsEcto-NAD+ glycohydrolase (CD38 molecule)
KeywordsHYDROLASE / CD38 / cyclic ADP ribose / ecto-ADP-ribosyl cyclase / Glycosidase
Function / homology
Function and homology information


2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / metabolic process / positive regulation of B cell proliferation / transferase activity / plasma membrane
Similarity search - Function
ADP Ribosyl Cyclase; Chain A, domain 1 / ADP Ribosyl Cyclase; Chain A, domain 1 / ADP-ribosyl cyclase (CD38/157) / ADP-ribosyl cyclase / NAD(P)-binding Rossmann-like Domain / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsEgea, P.F. / Muller-Steffner, H. / Stroud, R.M. / Oppenheimer, N. / Kellenberger, E. / Schuber, F.
CitationJournal: Plos One / Year: 2012
Title: Insights into the mechanism of bovine CD38/NAD+glycohydrolase from the X-ray structures of its Michaelis complex and covalently-trapped intermediates.
Authors: Egea, P.F. / Muller-Steffner, H. / Kuhn, I. / Cakir-Kiefer, C. / Oppenheimer, N.J. / Stroud, R.M. / Kellenberger, E. / Schuber, F.
History
DepositionFeb 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 23, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ecto-NAD+ glycohydrolase (CD38 molecule)
B: Ecto-NAD+ glycohydrolase (CD38 molecule)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9299
Polymers56,6002
Non-polymers1,3297
Water8,791488
1
A: Ecto-NAD+ glycohydrolase (CD38 molecule)
hetero molecules

B: Ecto-NAD+ glycohydrolase (CD38 molecule)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9299
Polymers56,6002
Non-polymers1,3297
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area3170 Å2
ΔGint-47 kcal/mol
Surface area23000 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.033, 80.164, 152.536
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ecto-NAD+ glycohydrolase (CD38 molecule)


Mass: 28300.061 Da / Num. of mol.: 2 / Mutation: E218Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: CD38 / Production host: Pichia pastoris (fungus) / References: UniProt: Q9TTF5, NAD+ glycohydrolase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20-30% PEG 4000, 50-250mM Ammonium Sulfate, 100 mM sodium cacodylate or sodium acetate or MES at pH-6.0-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2007
RadiationProtocol: 1.11587 / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.51→80.1 Å / Num. all: 74734 / Num. obs: 74734 / % possible obs: 82 % / Redundancy: 3.3 % / Biso Wilson estimate: 21 Å2 / Rsym value: 0.035 / Net I/σ(I): 16.9
Reflection shellResolution: 1.51→1.61 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 4271 / Rsym value: 0.318 / % possible all: 33

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.4.0067refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YH3

1yh3


Resolution: 1.51→44.95 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.541 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2102 5756 7.7 %RANDOM
Rwork0.18717 ---
obs0.18894 68851 81.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.542 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.51→44.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3814 0 81 488 4383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0214223
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.9675761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0495531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.91622.741197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0515731
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9411546
X-RAY DIFFRACTIONr_chiral_restr0.0920.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213242
X-RAY DIFFRACTIONr_mcbond_it0.7811.52536
X-RAY DIFFRACTIONr_mcangle_it1.51624124
X-RAY DIFFRACTIONr_scbond_it2.46331687
X-RAY DIFFRACTIONr_scangle_it4.0624.51631
LS refinement shellResolution: 1.51→1.549 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.455 139 -
Rwork0.353 1524 -
obs--24.89 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.23160.13780.04570.687-0.1230.1230.0038-0.06360.0159-0.02980.0070.01020.01960.009-0.0108-0.02720.0055-0.004-0.0063-0.004-0.01311.18229.666630.1935
20.5035-0.1620.30440.53-0.42760.83570.02310.1113-0.10390.0063-0.00180.01270.00910.0228-0.0213-0.02350.0003-0.0094-0.0046-0.0175-0.039822.3911-1.99272.7018
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 277
2X-RAY DIFFRACTION1A501 - 502
3X-RAY DIFFRACTION2B39 - 275
4X-RAY DIFFRACTION2B501 - 502

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