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- PDB-4cyg: The structure of vanin-1: defining the link between metabolic dis... -

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Basic information

Entry
Database: PDB / ID: 4cyg
TitleThe structure of vanin-1: defining the link between metabolic disease, oxidative stress and inflammation
ComponentsPANTETHEINASE
KeywordsHYDROLASE / INFLAMMATION / COLITIS / COA BIOSYNTHESIS / OXIDATIVE STRESS
Function / homology
Function and homology information


pantetheine hydrolase / pantetheine hydrolase activity / pantothenate metabolic process / chronic inflammatory response / coenzyme A catabolic process / Vitamin B5 (pantothenate) metabolism / Post-translational modification: synthesis of GPI-anchored proteins / positive regulation of T cell differentiation in thymus / acute inflammatory response / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway ...pantetheine hydrolase / pantetheine hydrolase activity / pantothenate metabolic process / chronic inflammatory response / coenzyme A catabolic process / Vitamin B5 (pantothenate) metabolism / Post-translational modification: synthesis of GPI-anchored proteins / positive regulation of T cell differentiation in thymus / acute inflammatory response / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / azurophil granule membrane / side of membrane / cell-cell adhesion / response to oxidative stress / inflammatory response / innate immune response / Neutrophil degranulation / extracellular region / membrane / plasma membrane
Similarity search - Function
Biotinidase-like, eukaryotic / Biotinidase/VNN family / Vanin, C-terminal / Vanin C-terminal domain / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase ...Biotinidase-like, eukaryotic / Biotinidase/VNN family / Vanin, C-terminal / Vanin C-terminal domain / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Chem-RRV / Pantetheinase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBoersma, Y.L. / Newman, J. / Adams, T.E. / Sparrow, L. / Cowieson, N. / Lucent, D. / Krippner, G. / Bozaoglu, K. / Peat, T.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: The Structure of Vanin-1: A Key Enzyme Linking Metabolic Disease and Inflammation
Authors: Boersma, Y.L. / Newman, J. / Adams, T.E. / Cowieson, N. / Krippner, G. / Bozaoglu, K. / Peat, T.S.
History
DepositionApr 11, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.temp
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PANTETHEINASE
B: PANTETHEINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,20513
Polymers112,6502
Non-polymers2,55511
Water5,531307
1
A: PANTETHEINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7096
Polymers56,3251
Non-polymers1,3835
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PANTETHEINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4967
Polymers56,3251
Non-polymers1,1716
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.093, 120.093, 221.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PANTETHEINASE / PANTETHEINE HYDROLASE / TIFF66 / VASCULAR NON-INFLAMMATORY MOLECULE 1 / VANIN-1


Mass: 56325.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FLAG TAG AT THE N-TERMINUS OF THE PROTEIN OTHERWISE THE PROTEIN IS THE MATURE FORM FOUND NATURALLY.
Source: (gene. exp.) HOMO SAPIENS (human) / Description: DNA SYNTHESIZED / Cell line (production host): HUMAN EMBRYONIC KIDNEY / Production host: HOMO SAPIENS (human) / References: UniProt: O95497, pantetheine hydrolase

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Sugars , 2 types, 7 molecules

#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.: 1
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
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 311 molecules

#3: Chemical ChemComp-RRV / (2R)-2,4-dihydroxy-N-[(3S)-3-hydroxy-4-phenylbutyl]-3,3-dimethylbutanamide


Mass: 295.374 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25NO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsFLAG TAG AT N-TERMINUS INSTEAD OF SIGNAL PEPTIDE AND THE PRO-PEPTIDE AT THE C-TERMINUS HAS BEEN ...FLAG TAG AT N-TERMINUS INSTEAD OF SIGNAL PEPTIDE AND THE PRO-PEPTIDE AT THE C-TERMINUS HAS BEEN REMOVED TO GIVE THE MATURE PROTEIN.

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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: 3.88 Å3/Da / Density % sol: 68.3 % / Description: NONE
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: CRYSTALLIZATION CONDITIONS: PROTEIN AT 12 MG/ML IN 50 MM BIS-TRIS PH 6.5 WITH 50 MM NACL. RESERVOIR CONDITIONS WERE 21% PEG 1500 WITH 10% (V/V) MALATE-MES-TRIS BUFFER AT PH 6.3. DROPS WERE ...Details: CRYSTALLIZATION CONDITIONS: PROTEIN AT 12 MG/ML IN 50 MM BIS-TRIS PH 6.5 WITH 50 MM NACL. RESERVOIR CONDITIONS WERE 21% PEG 1500 WITH 10% (V/V) MALATE-MES-TRIS BUFFER AT PH 6.3. DROPS WERE 200 NL PLUS 200 NL IN SITTING DROP PLATES AT 8C.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→48.3 Å / Num. obs: 72390 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 14.9 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 15.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 15.2 % / Rmerge(I) obs: 1.24 / Mean I/σ(I) obs: 2.6 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CYF

4cyf


Resolution: 2.3→105.62 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.191 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY THE RR6 INHIBITOR LOOKS TO BE COVALENTLY BOUND TO THE ACTIVE SITE CYS211 AS THE DENSITY IS CONTINUOUS IN THAT REGION.
RfactorNum. reflection% reflectionSelection details
Rfree0.21444 3638 5 %RANDOM
Rwork0.18624 ---
obs0.18765 68703 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.863 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.3→105.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7267 0 168 307 7742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0197730
X-RAY DIFFRACTIONr_bond_other_d0.0020.027045
X-RAY DIFFRACTIONr_angle_refined_deg1.241.96710544
X-RAY DIFFRACTIONr_angle_other_deg0.82316210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5515941
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50824.622357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.708151187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5621529
X-RAY DIFFRACTIONr_chiral_restr0.070.21172
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218830
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021825
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9624.6953743
X-RAY DIFFRACTIONr_mcbond_other1.9594.6953742
X-RAY DIFFRACTIONr_mcangle_it3.1347.9154691
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5775.1673987
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 241 -
Rwork0.299 5003 -
obs--98.68 %

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