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- PDB-4gg2: The crystal structure of glutamate-bound human gamma-glutamyltran... -

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Basic information

Entry
Database: PDB / ID: 4gg2
TitleThe crystal structure of glutamate-bound human gamma-glutamyltranspeptidase 1
Components(Gamma-glutamyltranspeptidase 1 ...) x 2
KeywordsHYDROLASE / NTN-HYDROLYASE / GLUTATHIONINE METABOLISM / N-GLYCOSYLATION / EXTERIOR 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 / glutathione biosynthetic process / glutamate metabolic process / leukotriene metabolic process / Aflatoxin activation and detoxification / cysteine biosynthetic process / 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, small (S) subunit / Gamma-glutamyltranspeptidase, large (L) subunit, C-terminal domain / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase signature. / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase, large subunit, C-terminal domain / Gamma-glutamyltranspeptidase, small subunit / Serum Albumin; Chain A, Domain 1 / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal ...Gamma-glutamyltranspeptidase, small (S) subunit / Gamma-glutamyltranspeptidase, large (L) subunit, C-terminal domain / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase signature. / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase, large subunit, C-terminal domain / Gamma-glutamyltranspeptidase, small subunit / Serum Albumin; Chain A, Domain 1 / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / IODIDE ION / Glutathione hydrolase 1 proenzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsWest, M.B. / Chen, Y. / Wickham, S. / Heroux, A. / Cahill, K. / Hanigan, M.H. / Mooers, B.H.M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Novel Insights into Eukaryotic gamma-Glutamyltranspeptidase 1 from the Crystal Structure of the Glutamate-bound Human Enzyme.
Authors: West, M.B. / Chen, Y. / Wickham, S. / Heroux, A. / Cahill, K. / Hanigan, M.H. / Mooers, B.H.
History
DepositionAug 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Nov 27, 2013Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_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 1.4Sep 13, 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: Gamma-glutamyltranspeptidase 1 heavy chain
B: Gamma-glutamyltranspeptidase 1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,22819
Polymers58,5762
Non-polymers2,65217
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15860 Å2
ΔGint-67 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.717, 126.753, 104.629
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Gamma-glutamyltranspeptidase 1 ... , 2 types, 2 molecules AB

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


Mass: 38561.715 Da / Num. of mol.: 1 / Fragment: unp residues 28-380
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GGT, GGT1, hGGT1 / Production host: PICHIA (fungus)
References: UniProt: P19440, gamma-glutamyltransferase, glutathione gamma-glutamate hydrolase, leukotriene-C4 hydrolase
#2: Protein Gamma-glutamyltranspeptidase 1 light chain / GGT 1 / Gamma-glutamyltransferase 1 / Glutathione hydrolase 1 / Leukotriene-C4 hydrolase


Mass: 20014.438 Da / Num. of mol.: 1 / Fragment: unp residues 381-569
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GGT, GGT1, hGGT1 / Production host: PICHIA (fungus)
References: UniProt: P19440, gamma-glutamyltransferase, glutathione gamma-glutamate hydrolase, 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, 384 molecules

#4: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.85 Å3/Da / Density % sol: 56.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 15-25% PEG3350, 100 mM Ammonium chloride, 0.5 mM L-glutamate, 100 mM Na:Cacodylate pH 6.0 , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2011
RadiationMonochromator: Monochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→47.18 Å / Num. all: 35539 / Num. obs: 34317 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 18.5 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 31.3
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.563 / % possible all: 75.8

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHENIXmodel building
PHENIX(phenix.refine: dev_1120)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4GDX

4gdx


Resolution: 2.21→43.975 Å / SU ML: 0.23 / σ(F): 1.99 / Phase error: 18.22 / Stereochemistry target values: ML
Details: Used Bijvoet pairs in refinement. The statistics above are for the merged reflections.
RfactorNum. reflection% reflection
Rfree0.1833 1716 5 %
Rwork0.1398 --
obs0.142 32579 96.15 %
all-35537 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.21→43.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4024 0 99 373 4496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124260
X-RAY DIFFRACTIONf_angle_d1.3435804
X-RAY DIFFRACTIONf_dihedral_angle_d13.6061533
X-RAY DIFFRACTIONf_chiral_restr0.076676
X-RAY DIFFRACTIONf_plane_restr0.006755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2097-2.24270.2897980.23511685X-RAY DIFFRACTION60
2.2427-2.27780.27581440.21952186X-RAY DIFFRACTION79
2.2778-2.31510.26051350.20152351X-RAY DIFFRACTION84
2.3151-2.3550.22141240.17322610X-RAY DIFFRACTION92
2.355-2.39780.21851350.15232734X-RAY DIFFRACTION98
2.3978-2.4440.2071450.14122833X-RAY DIFFRACTION100
2.444-2.49380.23631650.13822813X-RAY DIFFRACTION100
2.4938-2.54810.21571490.13012755X-RAY DIFFRACTION100
2.5481-2.60730.2241280.13052862X-RAY DIFFRACTION100
2.6073-2.67250.19161480.1332816X-RAY DIFFRACTION100
2.6725-2.74480.20251550.12792834X-RAY DIFFRACTION100
2.7448-2.82550.20971350.13262790X-RAY DIFFRACTION100
2.8255-2.91670.17581170.13342836X-RAY DIFFRACTION100
2.9167-3.02090.20921570.13862803X-RAY DIFFRACTION100
3.0209-3.14190.17871260.13872814X-RAY DIFFRACTION100
3.1419-3.28480.20141540.142834X-RAY DIFFRACTION100
3.2848-3.45790.18221340.14222804X-RAY DIFFRACTION100
3.4579-3.67450.16511750.13672769X-RAY DIFFRACTION100
3.6745-3.9580.1431440.122814X-RAY DIFFRACTION100
3.958-4.3560.15741530.11022832X-RAY DIFFRACTION100
4.356-4.98560.13061720.10722787X-RAY DIFFRACTION100
4.9856-6.27840.19191580.14652792X-RAY DIFFRACTION100
6.2784-43.9840.18821240.1882840X-RAY DIFFRACTION100

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