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- PDB-2qm6: Crystal Structure of Helicobacter Pylori Gamma-Glutamyltranspepti... -

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Basic information

Entry
Database: PDB / ID: 2qm6
TitleCrystal Structure of Helicobacter Pylori Gamma-Glutamyltranspeptidase in Complex with Glutamate
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, 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 / Nucleophile aminohydrolases, N-terminal ...: / 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 / Nucleophile aminohydrolases, N-terminal / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
GLUTAMIC ACID / Glutathione hydrolase proenzyme
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBarycki, J.J. / Sand, A. / Boanca, G.
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 14, 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 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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)122,2696
Polymers121,9754
Non-polymers2942
Water13,277737
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)61,1353
Polymers60,9882
Non-polymers1471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11030 Å2
MethodPISA
3
C: Gamma-glutamyltranspeptidase
D: Gamma-glutamyltranspeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1353
Polymers60,9882
Non-polymers1471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.983, 104.762, 91.910
Angle α, β, γ (deg.)90.00, 91.85, 90.00
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: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2 / References: UniProt: O25743, gamma-glutamyltransferase
#2: Protein Gamma-glutamyltranspeptidase / Ggt


Mass: 20410.186 Da / Num. of mol.: 2 / Fragment: residues 380-567
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HP_1118 / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2 / References: UniProt: O25743, gamma-glutamyltransferase
#3: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 737 / 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: 2.17 Å3/Da / Density % sol: 43.29 %
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: 1.6→50 Å / Num. obs: 136302 / % possible obs: 99.4 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.075 / Rsym value: 0.088 / Net I/σ(I): 21.9
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.474 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2NQO

2nqo


Resolution: 1.6→32.93 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.697 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19017 13494 9.9 %RANDOM
Rwork0.16652 ---
obs0.16888 122321 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.361 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.03 Å2
2--0.42 Å20 Å2
3----0.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.085 Å0.088 Å
Luzzati sigma a0.05 Å-
Refinement stepCycle: LAST / Resolution: 1.6→32.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8050 0 20 737 8807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228305
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.9711237
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11351078
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34725.359334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.737151459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0061528
X-RAY DIFFRACTIONr_chiral_restr0.0830.21255
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026232
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.24026
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.25785
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2660
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6331.55472
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.93928550
X-RAY DIFFRACTIONr_scbond_it1.73733197
X-RAY DIFFRACTIONr_scangle_it2.7414.52687
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 1010 -
Rwork0.187 8992 -
obs--99.05 %
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)
11.5171-0.15750.28410.4878-0.03820.42730.01450.1112-0.1871-0.0872-0.00780.04930.0987-0.0747-0.0067-0.0016-0.0075-0.00030.0352-0.01620.032135.87-16.26129.137
20.8234-0.4139-0.11480.68150.23510.8833-0.0191-0.0576-0.01950.00590.0458-0.04960.03440.0845-0.02670.01830.00420.00160.04450.00570.039451.769-13.46838.792
30.3318-0.1376-0.02620.499-0.0550.5462-0.0403-0.047-0.0420.05450.05080.0557-0.0391-0.0257-0.01050.0114-0.00170.00080.04880.00020.015339.379-2.00240.532
40.48930.7109-0.12983.54121.68861.43930.05220.0960.2262-0.08340.0090.271-0.3769-0.412-0.06110.062-0.0004-0.01210.08740.01430.035140.0124.32937.665
50.3706-0.2244-0.1480.58830.17020.6429-0.0113-0.0359-0.00560.03840.0368-0.0319-0.02770.0444-0.02540.0113-0.00260.00550.03820.0030.017345-5.25740.572
60.59110.1062-0.02181.0858-0.09360.7874-0.04390.0566-0.0312-0.07910.06210.0373-0.0788-0.0342-0.01820.0409-0.0046-0.00270.064-0.00160.004137.9786.62924.617
724.643514.52811.90019.5632.3911.7644-0.35560.5694-0.8474-0.5280.4023-0.5238-0.05910.0713-0.04670.0512-0.0107-0.02180.0737-0.00360.066336.433-5.93319.867
80.76170.3095-0.1961.0377-0.2261.0082-0.0499-0.0087-0.1259-0.1327-0.0039-0.03220.11740.07760.05390.03450.02240.02180.02970.0070.036140.737-8.599-14.924
91.3340.4077-0.76431.7657-0.72681.8133-0.07850.0377-0.0789-0.13450.09750.16430.225-0.1353-0.0190.0265-0.0319-0.0173-0.0038-0.0060.039425.953-15.886-13.07
100.33160.148-0.04640.7369-0.01730.6793-0.01650.0025-0.0031-0.11430.04-0.0949-0.06730.1166-0.02360.0177-0.01030.01450.04490.0030.009146.61810.652-13.84
111.17090.2973-0.25090.217-0.64012.4015-0.01940.05410.1913-0.04520.0394-0.0417-0.19060.0326-0.02010.0629-0.02560.0142-0.00140.00370.027644.61827.167-12.958
120.58640.2313-0.190.765-0.25950.8613-0.0066-0.0039-0.0158-0.10510.00780.02690.0001-0.017-0.00130.02820.0130.00090.0192-0.00060.010236.744-0.149-16.026
130.6409-0.1941-0.20381.20450.18740.7751-0.013-0.1031-0.04730.1020.0234-0.0596-0.01790.1141-0.01030.0173-0.0033-0.00720.07610.01430.00744.368.2261.63
1436.3794-29.8022-3.176725.16440.54415.9243-1.1543-1.0423-0.20550.88510.8850.46880.30310.23960.26930.1020.0257-0.01910.07990.01080.080242.756-3.4144.557
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA32 - 9530 - 93
2X-RAY DIFFRACTION2AA96 - 20694 - 204
3X-RAY DIFFRACTION3AA207 - 355205 - 353
4X-RAY DIFFRACTION4AA356 - 372354 - 370
5X-RAY DIFFRACTION5BB380 - 4581 - 79
6X-RAY DIFFRACTION6BB459 - 55580 - 176
7X-RAY DIFFRACTION7BB556 - 565177 - 186
8X-RAY DIFFRACTION8CC32 - 16230 - 160
9X-RAY DIFFRACTION9CC163 - 245161 - 243
10X-RAY DIFFRACTION10CC246 - 352244 - 350
11X-RAY DIFFRACTION11CC353 - 379351 - 377
12X-RAY DIFFRACTION12DD380 - 4581 - 79
13X-RAY DIFFRACTION13DD459 - 55780 - 178
14X-RAY DIFFRACTION14DD558 - 565179 - 186

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