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- PDB-4gdx: Crystal Structure of Human Gamma-Glutamyl Transpeptidase--Glutama... -

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Basic information

Entry
Database: PDB / ID: 4gdx
TitleCrystal Structure of Human Gamma-Glutamyl Transpeptidase--Glutamate complex
Components(Gamma-glutamyltranspeptidase 1 ...) x 2
KeywordsHYDROLASE / product-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 / 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 / Glutathione hydrolase 1 proenzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 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 1, 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 / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
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)63,00012
Polymers61,4322
Non-polymers1,56810
Water10,791599
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15790 Å2
ΔGint-158 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.524, 125.247, 104.468
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: 40874.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GGT, GGT1 / 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: 20556.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GGT, GGT1 / 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, 603 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-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 599 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE UNP P19440 HAS VAL272 WHEN THIS STRUCTURE HAS ALA272. ALA272 IS A NATURAL VARIANT ON THIS HUMAN ...THE UNP P19440 HAS VAL272 WHEN THIS STRUCTURE HAS ALA272. ALA272 IS A NATURAL VARIANT ON THIS HUMAN PROTEIN. THE SEQUENCE OF THIS VARIANT IS GIVEN BY GENBANK AAA52546.1

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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: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 17.5% PEG3350, 100 mM Ammonium chloride, 0.5 mM L-glutamate, and 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
Details: A Si-111 double crystal monochromator that provides a broad range 7-15 keV (0.8 2-1.8 ) x-rays. The undulator beam is focused vertically by a Rh-coated mirror.
RadiationMonochromator: A Si-111 double crystal monochromator that provides a broad range 7-15 keV (0.82-1.8 ) x-rays. The undulator beam is focused vertically by a Rh-coated mirror.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.67→47.07 Å / Num. all: 70751 / Num. obs: 70751 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 16.2
Reflection shellResolution: 1.67→1.76 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.74 / % possible all: 90.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: dev_1108)refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2DBU

2dbu


Resolution: 1.67→47.07 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 17.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1745 3970 5.05 %
Rwork0.1451 --
obs0.1466 70751 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.67→47.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4037 0 92 599 4728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014466
X-RAY DIFFRACTIONf_angle_d1.2616105
X-RAY DIFFRACTIONf_dihedral_angle_d13.0721633
X-RAY DIFFRACTIONf_chiral_restr0.076704
X-RAY DIFFRACTIONf_plane_restr0.007802
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6696-1.690.2861170.25552116X-RAY DIFFRACTION80
1.69-1.71140.2951050.24362387X-RAY DIFFRACTION88
1.7114-1.73390.25581430.23162520X-RAY DIFFRACTION94
1.7339-1.75760.24271300.21752582X-RAY DIFFRACTION96
1.7576-1.78270.26031270.20682656X-RAY DIFFRACTION97
1.7827-1.80930.21481340.18892641X-RAY DIFFRACTION97
1.8093-1.83760.20741580.18522593X-RAY DIFFRACTION98
1.8376-1.86780.21351360.17692702X-RAY DIFFRACTION99
1.8678-1.90.19551410.16792697X-RAY DIFFRACTION100
1.9-1.93450.19531480.16372663X-RAY DIFFRACTION100
1.9345-1.97170.19441720.15782634X-RAY DIFFRACTION100
1.9717-2.0120.1931510.15222735X-RAY DIFFRACTION100
2.012-2.05570.18331350.15142687X-RAY DIFFRACTION100
2.0557-2.10350.19231630.14252713X-RAY DIFFRACTION100
2.1035-2.15610.17761430.13392688X-RAY DIFFRACTION100
2.1561-2.21440.15841310.12742725X-RAY DIFFRACTION100
2.2144-2.27960.16291380.12382711X-RAY DIFFRACTION100
2.2796-2.35320.16371500.12212688X-RAY DIFFRACTION100
2.3532-2.43730.16731610.12142709X-RAY DIFFRACTION100
2.4373-2.53480.1731480.12612700X-RAY DIFFRACTION100
2.5348-2.65020.15441390.12052735X-RAY DIFFRACTION100
2.6502-2.78990.14551450.11812711X-RAY DIFFRACTION100
2.7899-2.96470.16121490.12672736X-RAY DIFFRACTION100
2.9647-3.19350.1481180.13442767X-RAY DIFFRACTION100
3.1935-3.51480.14431390.13612767X-RAY DIFFRACTION100
3.5148-4.02320.15491630.12722748X-RAY DIFFRACTION100
4.0232-5.06790.1591340.12562797X-RAY DIFFRACTION100
5.0679-47.09180.20341520.19872902X-RAY DIFFRACTION100

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