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- PDB-6gq3: Human asparagine synthetase (ASNS) in complex with 6-diazo-5-oxo-... -

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Basic information

Entry
Database: PDB / ID: 6gq3
TitleHuman asparagine synthetase (ASNS) in complex with 6-diazo-5-oxo-L-norleucine (DON) at 1.85 A resolution
ComponentsAsparagine synthetase [glutamine-hydrolyzing]
KeywordsBIOSYNTHETIC PROTEIN / L-asparagine biosynthesis / breast cancer / inhibitor development
Function / homology
Function and homology information


asparagine synthase (glutamine-hydrolysing) / L-asparagine biosynthetic process / asparagine synthase (glutamine-hydrolyzing) activity / : / Response of EIF2AK1 (HRI) to heme deficiency / Aspartate and asparagine metabolism / ATF4 activates genes in response to endoplasmic reticulum stress / Response of EIF2AK4 (GCN2) to amino acid deficiency / cellular response to glucose starvation / positive regulation of mitotic cell cycle ...asparagine synthase (glutamine-hydrolysing) / L-asparagine biosynthetic process / asparagine synthase (glutamine-hydrolyzing) activity / : / Response of EIF2AK1 (HRI) to heme deficiency / Aspartate and asparagine metabolism / ATF4 activates genes in response to endoplasmic reticulum stress / Response of EIF2AK4 (GCN2) to amino acid deficiency / cellular response to glucose starvation / positive regulation of mitotic cell cycle / negative regulation of apoptotic process / ATP binding / cytosol
Similarity search - Function
Asparagine synthase, glutamine-hydrolyzing / Asparagine synthase, N-terminal domain / : / Glutamine amidotransferase domain / Asparagine synthase / Asparagine synthase / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / HUPs / Nucleophile aminohydrolases, N-terminal ...Asparagine synthase, glutamine-hydrolyzing / Asparagine synthase, N-terminal domain / : / Glutamine amidotransferase domain / Asparagine synthase / Asparagine synthase / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / HUPs / Nucleophile aminohydrolases, N-terminal / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5-OXO-L-NORLEUCINE / Asparagine synthetase [glutamine-hydrolyzing]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsZhu, W. / Radadiya, A. / Bisson, C. / Jin, Y. / Nordin, B.E. / Imasaki, T. / Wenzel, S. / Sedelnikova, S.E. / Berry, A.H. / Nomanbhoy, T.K. ...Zhu, W. / Radadiya, A. / Bisson, C. / Jin, Y. / Nordin, B.E. / Imasaki, T. / Wenzel, S. / Sedelnikova, S.E. / Berry, A.H. / Nomanbhoy, T.K. / Kozarich, J.W. / Takagi, Y. / Rice, D.W. / Richards, N.G.J.
CitationJournal: Commun Biol / Year: 2019
Title: High-resolution crystal structure of human asparagine synthetase enables analysis of inhibitor binding and selectivity.
Authors: Zhu, W. / Radadiya, A. / Bisson, C. / Wenzel, S. / Nordin, B.E. / Martinez-Marquez, F. / Imasaki, T. / Sedelnikova, S.E. / Coricello, A. / Baumann, P. / Berry, A.H. / Nomanbhoy, T.K. / ...Authors: Zhu, W. / Radadiya, A. / Bisson, C. / Wenzel, S. / Nordin, B.E. / Martinez-Marquez, F. / Imasaki, T. / Sedelnikova, S.E. / Coricello, A. / Baumann, P. / Berry, A.H. / Nomanbhoy, T.K. / Kozarich, J.W. / Jin, Y. / Rice, D.W. / Takagi, Y. / Richards, N.G.J.
History
DepositionJun 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Asparagine synthetase [glutamine-hydrolyzing]
B: Asparagine synthetase [glutamine-hydrolyzing]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,99812
Polymers128,9122
Non-polymers1,08610
Water10,233568
1
A: Asparagine synthetase [glutamine-hydrolyzing]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0617
Polymers64,4561
Non-polymers6056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Asparagine synthetase [glutamine-hydrolyzing]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9375
Polymers64,4561
Non-polymers4814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.700, 83.520, 110.290
Angle α, β, γ (deg.)90.00, 90.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Asparagine synthetase [glutamine-hydrolyzing] / Cell cycle control protein TS11 / Glutamine-dependent asparagine synthetase


Mass: 64455.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Missing loops: 210-223 and 466-480. No electron density for C-terminus: 535-561
Source: (gene. exp.) Homo sapiens (human) / Gene: ASNS, TS11 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P08243, asparagine synthase (glutamine-hydrolysing)

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Non-polymers , 5 types, 578 molecules

#2: Chemical ChemComp-ONL / 5-OXO-L-NORLEUCINE


Type: L-peptide linking / Mass: 145.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11NO3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 2.31 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M NaCl, 0.1 M sodium HEPES buffer, pH 7.5, and 12% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→33.65 Å / Num. obs: 100002 / % possible obs: 99.8 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.067 / Net I/σ(I): 9.7
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4932 / CC1/2: 0.512 / Rpim(I) all: 0.624 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CT9

1ct9


Resolution: 1.85→33.65 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.395 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22462 4875 4.9 %RANDOM
Rwork0.17764 ---
obs0.17991 95104 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.556 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20 Å2-0.44 Å2
2---0.19 Å20 Å2
3----1.25 Å2
Refinement stepCycle: 1 / Resolution: 1.85→33.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8244 0 68 568 8880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198543
X-RAY DIFFRACTIONr_bond_other_d0.0020.027903
X-RAY DIFFRACTIONr_angle_refined_deg1.391.96511543
X-RAY DIFFRACTIONr_angle_other_deg1.479318333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27151022
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00123.61410
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.664151469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5781552
X-RAY DIFFRACTIONr_chiral_restr0.0830.21240
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219390
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021822
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_it24.5142.9964085
X-RAY DIFFRACTIONr_mcbond_other24.5172.9964084
X-RAY DIFFRACTIONr_mcangle_it21.2594.445096
X-RAY DIFFRACTIONr_mcangle_other21.2574.4395097
X-RAY DIFFRACTIONr_scbond_it29.5693.6444458
X-RAY DIFFRACTIONr_scbond_other29.5693.6444458
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other26.1265.1156444
X-RAY DIFFRACTIONr_long_range_B_refined26.18635.8169618
X-RAY DIFFRACTIONr_long_range_B_other26.18435.8179619
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 371 -
Rwork0.307 6982 -
obs--99.86 %

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