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- PDB-2qmc: Crystal Structure of Helicobacter Pylori Gamma-Glutamyltranspepti... -

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Basic information

Entry
Database: PDB / ID: 2qmc
TitleCrystal Structure of Helicobacter Pylori Gamma-Glutamyltranspeptidase T380A Mutant
Components(Gamma-glutamyltranspeptidase) x 2
KeywordsTRANSFERASE / NTN-HYDROLASE / GLUTAMYLTRANSPEPTIDASE
Function / homology
Function and homology information


gamma-glutamyltransferase / glutathione gamma-glutamate hydrolase / glutathione hydrolase activity / leukotriene C4 gamma-glutamyl transferase activity / glutathione catabolic process / negative regulation of cell cycle G1/S phase transition / glutathione biosynthetic process / negative regulation of T cell proliferation / positive regulation of interleukin-8 production
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 ...: / 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
S-(P-NITROBENZYL)GLUTATHIONE / Glutathione hydrolase proenzyme
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsBarycki, J.J. / Boanca, G. / Sand, A.
Citation
Journal: Biochemistry / Year: 2007
Title: Characterization of Helicobacter pylori gamma-glutamyltranspeptidase reveals the molecular basis for substrate specificity and a critical role for the tyrosine 433-containing loop in catalysis.
Authors: Morrow, A.L. / Williams, K. / Sand, A. / Boanca, G. / Barycki, J.J.
#1: Journal: J.Biol.Chem. / Year: 2007
Title: Autoprocessing of Helicobacter pylori gamma-glutamyltranspeptidase leads to the formation of a threonine-threonine catalytic dyad.
Authors: Boanca, G. / Sand, A. / Okada, T. / Suzuki, H. / Kumagai, H. / Fukuyama, K. / Barycki, J.J.
History
DepositionJul 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-glutamyltranspeptidase
B: Gamma-glutamyltranspeptidase
C: Gamma-glutamyltranspeptidase
D: Gamma-glutamyltranspeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,8006
Polymers121,9154
Non-polymers8852
Water10,593588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Gamma-glutamyltranspeptidase
B: Gamma-glutamyltranspeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4003
Polymers60,9582
Non-polymers4421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11620 Å2
MethodPISA
3
C: Gamma-glutamyltranspeptidase
D: Gamma-glutamyltranspeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4003
Polymers60,9582
Non-polymers4421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.140, 106.674, 87.194
Angle α, β, γ (deg.)90.000, 104.960, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Gamma-glutamyltranspeptidase / Ggt


Mass: 40577.379 Da / Num. of mol.: 2 / Fragment: residues 25-379
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HP_1118 / Plasmid: pDUET / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2 / References: UniProt: O25743, gamma-glutamyltransferase
#2: Protein Gamma-glutamyltranspeptidase / Ggt


Mass: 20380.160 Da / Num. of mol.: 2 / Fragment: residues 380-567 / Mutation: T380A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HP_1118 / Plasmid: pDUET / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2 / References: UniProt: O25743, gamma-glutamyltransferase
#3: Chemical ChemComp-GTB / S-(P-NITROBENZYL)GLUTATHIONE


Mass: 442.444 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H22N4O8S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 588 / 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: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200 MM HEPES, 25% PEG MME2000, 5 MG/ML PROTEIN, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 135161 / % possible obs: 93.2 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.084 / Rsym value: 0.068 / Χ2: 1.042 / Net I/σ(I): 21.3
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 5 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2.59 / Num. unique all: 12852 / Rsym value: 0.413 / Χ2: 0.813 / % possible all: 89

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2NQO

2nqo


Resolution: 1.55→33.35 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.356 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.218 13319 9.9 %RANDOM
Rwork0.187 ---
obs0.19 134438 92.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.126 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å20.03 Å2
2---1.25 Å20 Å2
3----0.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.096 Å0.098 Å
Luzzati sigma a0.062 Å-
Refinement stepCycle: LAST / Resolution: 1.55→33.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8029 0 30 588 8647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228248
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.97211153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13251067
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83625.274328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.449151434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7981528
X-RAY DIFFRACTIONr_chiral_restr0.0860.21248
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026172
X-RAY DIFFRACTIONr_nbd_refined0.1960.24112
X-RAY DIFFRACTIONr_nbtor_refined0.3040.25777
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1010.2561
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.231
X-RAY DIFFRACTIONr_mcbond_it0.6851.55413
X-RAY DIFFRACTIONr_mcangle_it0.99328466
X-RAY DIFFRACTIONr_scbond_it1.8633190
X-RAY DIFFRACTIONr_scangle_it2.8644.52687
LS refinement shellResolution: 1.55→1.593 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 918 -
Rwork0.22 8423 -
all-9341 -
obs--87.26 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.05270.1664-0.39041.0189-0.18391.6227-0.04130.00670.0191-0.06240.0179-0.0202-0.11810.04640.0234-0.11750.0134-0.0234-0.0765-0.0134-0.087227.261314.594928.2256
21.6468-0.122-0.04230.8813-0.39391.7277-0.04380.01030.0619-0.04810.06340.0834-0.1544-0.2004-0.0197-0.04910.0467-0.0208-0.0325-0.0255-0.083716.963219.427631.5255
30.4863-0.1975-0.00151.2730.41650.8461-0.0385-0.06280.0270.05630.0828-0.0623-0.0058-0.0014-0.0443-0.11820.00540.0002-0.03260.0212-0.115626.67276.267132.1227
41.47160.6407-0.97133.37911.22632.15730.0463-0.0179-0.34070.1313-0.0159-0.42880.33670.3268-0.03040.04480.0163-0.0069-0.02170.04050.03426.9733-21.606330.3581
50.6396-0.1038-0.09740.86230.17181.162-0.0633-0.1069-0.03580.06740.04580.02970.0415-0.04610.0176-0.12310.0202-0.0124-0.04180.0041-0.106223.84678.283833.9731
60.64880.22270.08482.35310.06221.0524-0.0660.07520.0078-0.17180.10840.02830.0781-0.0276-0.0425-0.0884-0.0027-0.0193-0.0340.0032-0.112823.8427-4.316217.244
719.724413.2923-7.39648.9714-5.17755.4998-0.03270.58770.7339-0.40480.45550.397-0.1144-0.4376-0.42270.0008-0.0003-0.007-0.02520.0590.000624.25258.187711.5234
81.54680.0197-0.31891.3295-0.04621.62350.19630.1410.40360.1429-0.00950.1427-0.231-0.0969-0.1868-0.01450.05560.1054-0.0510.10480.11919.48349.0099-18.4786
92.56211.0813-0.39941.865-0.24411.13720.1550.10940.50550.37120.01140.1245-0.22220.1515-0.16640.15170.03090.1051-0.02690.09880.15821.231616.8523-17.2354
101.16460.3129-0.14350.9169-0.5281.05410.13620.21570.2684-0.00650.08440.2182-0.0591-0.1972-0.2206-0.06910.05610.0373-0.00520.05690.01145.4681-0.2452-18.8789
113.371-0.5853-0.83361.81110.66410.36390.1166-0.0029-0.1608-0.0092-0.06770.32570.5092-0.2253-0.04890.0509-0.0536-0.04560.0112-0.01730.06053.5119-24.342-14.3971
121.32420.2101-0.21790.7446-0.50081.06360.15410.20570.25070.04760.01650.1258-0.0817-0.0198-0.1706-0.05790.0590.0608-0.0320.08020.01610.85352.5319-20.493
131.3824-0.0456-0.21921.3346-0.32161.64240.1941-0.1390.17790.13060.01150.0488-0.0703-0.0512-0.2055-0.0447-0.02620.0242-0.0567-0.0098-0.043310.9258-6.6758-1.8836
1410.8701-12.9556-0.806116.00341.2910.2538-0.4905-0.8450.0490.40740.4731-0.0712-0.2432-0.07080.01740.14770.02410.10570.1208-0.07660.08848.14367.80581.8664
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA32 - 12230 - 120
2X-RAY DIFFRACTION2AA123 - 196121 - 194
3X-RAY DIFFRACTION3AA197 - 353195 - 351
4X-RAY DIFFRACTION4AA354 - 372352 - 370
5X-RAY DIFFRACTION5BB380 - 4591 - 80
6X-RAY DIFFRACTION6BB460 - 55581 - 176
7X-RAY DIFFRACTION7BB556 - 565177 - 186
8X-RAY DIFFRACTION8CC32 - 14130 - 139
9X-RAY DIFFRACTION9CC142 - 211140 - 209
10X-RAY DIFFRACTION10CC212 - 349210 - 347
11X-RAY DIFFRACTION11CC350 - 379348 - 377
12X-RAY DIFFRACTION12DD380 - 4591 - 80
13X-RAY DIFFRACTION13DD460 - 55381 - 174
14X-RAY DIFFRACTION14DD554 - 565175 - 186

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