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- PDB-5jyo: Allosteric inhibition of Kidney Isoform of Glutaminase -

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Basic information

Entry
Database: PDB / ID: 5jyo
TitleAllosteric inhibition of Kidney Isoform of Glutaminase
ComponentsGlutaminase kidney isoform, mitochondrial
KeywordsHYDROLASE / KGA / GAC / allosteric inhibition / Warburg effect
Function / homology
Function and homology information


glutamine catabolic process / glutamate biosynthetic process / regulation of respiratory gaseous exchange by nervous system process / Glutamate and glutamine metabolism / intracellular glutamate homeostasis / Glutamate Neurotransmitter Release Cycle / glutaminase / glutaminase activity / suckling behavior / TP53 Regulates Metabolic Genes ...glutamine catabolic process / glutamate biosynthetic process / regulation of respiratory gaseous exchange by nervous system process / Glutamate and glutamine metabolism / intracellular glutamate homeostasis / Glutamate Neurotransmitter Release Cycle / glutaminase / glutaminase activity / suckling behavior / TP53 Regulates Metabolic Genes / chemical synaptic transmission / protein homotetramerization / mitochondrial matrix / synapse / mitochondrion / cytosol
Similarity search - Function
Glutaminase, EF-hand domain / EF-hand domain / Glutaminase / Glutaminase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats ...Glutaminase, EF-hand domain / EF-hand domain / Glutaminase / Glutaminase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-63J / Glutaminase kidney isoform, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.098 Å
AuthorsSivaraman, J. / Jayaraman, S.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)Tier-2 grant R154-000-625-112 Singapore
CitationJournal: Oncotarget / Year: 2016
Title: Structural basis for exploring the allosteric inhibition of human kidney type glutaminase.
Authors: Ramachandran, S. / Pan, C.Q. / Zimmermann, S.C. / Duvall, B. / Tsukamoto, T. / Low, B.C. / Sivaraman, J.
History
DepositionMay 15, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Derived calculations
Revision 1.2Dec 25, 2019Group: Advisory / Author supporting evidence / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_audit_support.funding_organization
Revision 1.3Nov 8, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
D: Glutaminase kidney isoform, mitochondrial
A: Glutaminase kidney isoform, mitochondrial
B: Glutaminase kidney isoform, mitochondrial
C: Glutaminase kidney isoform, mitochondrial
E: Glutaminase kidney isoform, mitochondrial
F: Glutaminase kidney isoform, mitochondrial
G: Glutaminase kidney isoform, mitochondrial
H: Glutaminase kidney isoform, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,36412
Polymers293,0788
Non-polymers2,2864
Water22,2851237
1
D: Glutaminase kidney isoform, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2062
Polymers36,6351
Non-polymers5721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glutaminase kidney isoform, mitochondrial


Theoretical massNumber of molelcules
Total (without water)36,6351
Polymers36,6351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Glutaminase kidney isoform, mitochondrial


Theoretical massNumber of molelcules
Total (without water)36,6351
Polymers36,6351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Glutaminase kidney isoform, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2062
Polymers36,6351
Non-polymers5721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Glutaminase kidney isoform, mitochondrial


Theoretical massNumber of molelcules
Total (without water)36,6351
Polymers36,6351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Glutaminase kidney isoform, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7783
Polymers36,6351
Non-polymers1,1432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Glutaminase kidney isoform, mitochondrial


Theoretical massNumber of molelcules
Total (without water)36,6351
Polymers36,6351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Glutaminase kidney isoform, mitochondrial


Theoretical massNumber of molelcules
Total (without water)36,6351
Polymers36,6351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
D: Glutaminase kidney isoform, mitochondrial
B: Glutaminase kidney isoform, mitochondrial
C: Glutaminase kidney isoform, mitochondrial
E: Glutaminase kidney isoform, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,6826
Polymers146,5394
Non-polymers1,1432
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
A: Glutaminase kidney isoform, mitochondrial

F: Glutaminase kidney isoform, mitochondrial
hetero molecules

G: Glutaminase kidney isoform, mitochondrial

H: Glutaminase kidney isoform, mitochondrial


Theoretical massNumber of molelcules
Total (without water)147,6826
Polymers146,5394
Non-polymers1,1432
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_445x-1,y-1,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_444x-1,y-1,z-11
MethodPISA
Unit cell
Length a, b, c (Å)126.404, 126.629, 126.269
Angle α, β, γ (deg.)112.88, 102.81, 112.74
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Glutaminase kidney isoform, mitochondrial / GLS / K-glutaminase / L-glutamine amidohydrolase


Mass: 36634.742 Da / Num. of mol.: 8 / Fragment: UNP RESIDUES 221-533
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLS, GLS1, KIAA0838 / Production host: Escherichia coli (E. coli) / References: UniProt: O94925, glutaminase
#2: Chemical
ChemComp-63J / 2-(pyridin-2-yl)-N-(5-{4-[6-({[3-(trifluoromethoxy)phenyl]acetyl}amino)pyridazin-3-yl]butyl}-1,3,4-thiadiazol-2-yl)acetamide


Mass: 571.574 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H24F3N7O3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1237 / 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: 5.27 Å3/Da / Density % sol: 76.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris propane (pH 7), 3% DMSO, 1.8 M LiSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 337350 / % possible obs: 96.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 15.32
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.448 / % possible all: 93.9

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Processing

Software
NameVersionClassification
PHENIX(dev_2420)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VOZ

3voz


Resolution: 2.098→21.361 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 22.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.213 1981 59 %
Rwork0.1897 --
obs0.1899 337267 96.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.098→21.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19088 0 160 1237 20485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00819724
X-RAY DIFFRACTIONf_angle_d0.84426663
X-RAY DIFFRACTIONf_dihedral_angle_d14.56611609
X-RAY DIFFRACTIONf_chiral_restr0.0492851
X-RAY DIFFRACTIONf_plane_restr0.0063464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0984-2.15090.27061290.265722731X-RAY DIFFRACTION91
2.1509-2.20890.27471430.236623846X-RAY DIFFRACTION97
2.2089-2.27390.26761410.216224033X-RAY DIFFRACTION97
2.2739-2.34720.21171450.211424204X-RAY DIFFRACTION97
2.3472-2.4310.30751380.220524131X-RAY DIFFRACTION97
2.431-2.52810.21811600.212824152X-RAY DIFFRACTION97
2.5281-2.6430.33021370.20924204X-RAY DIFFRACTION97
2.643-2.78210.22091370.204424121X-RAY DIFFRACTION98
2.7821-2.9560.23391480.214224276X-RAY DIFFRACTION98
2.956-3.18350.21851490.202824321X-RAY DIFFRACTION98
3.1835-3.50260.24621360.188324340X-RAY DIFFRACTION98
3.5026-4.00660.15881360.167824168X-RAY DIFFRACTION98
4.0066-5.03690.18131440.157223635X-RAY DIFFRACTION95
5.0369-21.36220.20041380.186123124X-RAY DIFFRACTION93

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