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- PDB-6xpc: Structure of human GGT1 in complex with full GSH molecule -

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Basic information

Entry
Database: PDB / ID: 6xpc
TitleStructure of human GGT1 in complex with full GSH molecule
Components(Glutathione hydrolase 1 ...) x 2
KeywordsHYDROLASE / Substrate-ENZYME COMPLEX / NTN-HYDROLASE FAMILY / GLYCOPROTEIN / N-GLYCOSYLATION / CELL SURFACE
Function / homology
Function and homology information


leukotriene-C4 hydrolase / peptidyltransferase activity / leukotriene-C(4) hydrolase / leukotriene D4 biosynthetic process / Defective GGT1 causes GLUTH / Defective GGT1 in aflatoxin detoxification causes GLUTH / LTC4-CYSLTR mediated IL4 production / Glutathione synthesis and recycling / peptide modification / gamma-glutamyltransferase ...leukotriene-C4 hydrolase / peptidyltransferase activity / leukotriene-C(4) hydrolase / leukotriene D4 biosynthetic process / Defective GGT1 causes GLUTH / Defective GGT1 in aflatoxin detoxification causes GLUTH / LTC4-CYSLTR mediated IL4 production / Glutathione synthesis and recycling / peptide modification / gamma-glutamyltransferase / glutathione gamma-glutamate hydrolase / glutathione hydrolase activity / leukotriene C4 gamma-glutamyl transferase activity / glutathione catabolic process / glutamate metabolic process / glutathione biosynthetic process / leukotriene metabolic process / cysteine biosynthetic process / Aflatoxin activation and detoxification / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of immune system process / Paracetamol ADME / zymogen activation / amino acid metabolic process / fatty acid metabolic process / regulation of inflammatory response / spermatogenesis / proteolysis / extracellular space / extracellular exosome / plasma membrane
Similarity search - Function
Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase signature. / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase, large subunit, C-terminal domain / Gamma-glutamyltranspeptidase, small subunit / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
GLUTATHIONE / Glutathione hydrolase 1 proenzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.26 Å
AuthorsTerzyan, S.S. / Hanigan, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM125952 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Crystal structures of glutathione- and inhibitor-bound human GGT1: critical interactions within the cysteinylglycine binding site.
Authors: Terzyan, S.S. / Nguyen, L.T. / Burgett, A.W.G. / Heroux, A. / Smith, C.A. / You, Y. / Hanigan, M.H.
History
DepositionJul 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: 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

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Assembly

Deposited unit
A: Glutathione hydrolase 1 heavy chain
B: Glutathione hydrolase 1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,27712
Polymers58,5482
Non-polymers1,72810
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15460 Å2
ΔGint-97 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.395, 124.679, 104.989
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-786-

HOH

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Components

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Glutathione hydrolase 1 ... , 2 types, 2 molecules AB

#1: Protein Glutathione hydrolase 1 heavy chain / / GGT 1 / Gamma-glutamyltransferase 1 / Glutathione hydrolase 1 / Leukotriene-C4 hydrolase


Mass: 38533.664 Da / Num. of mol.: 1 / Mutation: V272A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GGT1, GGT / Plasmid: PPICZAA / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33
References: UniProt: P19440, glutathione gamma-glutamate hydrolase, gamma-glutamyltransferase, leukotriene-C4 hydrolase
#2: Protein Glutathione hydrolase 1 light chain / / GGT 1 / Gamma-glutamyltransferase 1 / Glutathione hydrolase 1 / Leukotriene-C4 hydrolase


Mass: 20014.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GGT1, GGT / Plasmid: PPICZAA / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33
References: UniProt: P19440, glutathione gamma-glutamate hydrolase, gamma-glutamyltransferase, leukotriene-C4 hydrolase

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Sugars , 1 types, 6 molecules

#3: 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 , 4 types, 251 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.93 Å3/Da / Density % sol: 58.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20-25%PEG3350, 0.1M ammonium cloride, 0.1M sodium cacodilate pH 6.0
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2016 / Details: mirror
RadiationMonochromator: SI 111 DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.26→20 Å / Num. obs: 32583 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 6.47 % / Biso Wilson estimate: 47.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.01
Reflection shellResolution: 2.26→2.39 Å / Redundancy: 6.08 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.52 / Num. unique obs: 4931 / % possible all: 93.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4GDX

4gdx


Resolution: 2.26→19.96 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.361 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2101 1630 5 %RANDOM
Rwork0.1594 ---
obs0.1619 30953 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 129.05 Å2 / Biso mean: 42.886 Å2 / Biso min: 13.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0 Å2
2---0.04 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 2.26→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4046 0 107 247 4400
Biso mean--69.83 47.95 -
Num. residues----531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194334
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.9785909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.825554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12123.439189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.41415685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6291535
X-RAY DIFFRACTIONr_chiral_restr0.0820.2682
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213320
LS refinement shellResolution: 2.26→2.318 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 116 -
Rwork0.294 2197 -
all-2313 -
obs--99.44 %

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