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- PDB-3fnm: Crystal structure of acivicin-inhibited gamma-glutamyltranspeptid... -

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Basic information

Entry
Database: PDB / ID: 3fnm
TitleCrystal structure of acivicin-inhibited gamma-glutamyltranspeptidase reveals critical roles for its C-terminus in autoprocessing and catalysis
Components
  • Gamma-glutamyltranspeptidase (Ggt) Large subunit
  • Gamma-glutamyltranspeptidase (Ggt) Small subunit
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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-AVN / Glutathione hydrolase proenzyme
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsWilliams, K. / Cullati, S. / Sand, A. / Biterova, E.I. / Barycki, J.J.
CitationJournal: Biochemistry / Year: 2009
Title: Crystal Structure of Acivicin-Inhibited gamma-Glutamyltranspeptidase Reveals Critical Roles for Its C-Terminus in Autoprocessing and Catalysis.
Authors: Williams, K. / Cullati, S. / Sand, A. / Biterova, E.I. / Barycki, J.J.
History
DepositionDec 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 9, 2012Group: Other
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-glutamyltranspeptidase (Ggt) Large subunit
B: Gamma-glutamyltranspeptidase (Ggt) Small subunit
C: Gamma-glutamyltranspeptidase (Ggt) Large subunit
D: Gamma-glutamyltranspeptidase (Ggt) Small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,3326
Polymers121,9754
Non-polymers3572
Water9,620534
1
A: Gamma-glutamyltranspeptidase (Ggt) Large subunit
B: Gamma-glutamyltranspeptidase (Ggt) Small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1663
Polymers60,9882
Non-polymers1791
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11620 Å2
ΔGint-68 kcal/mol
Surface area19380 Å2
MethodPISA
2
C: Gamma-glutamyltranspeptidase (Ggt) Large subunit
D: Gamma-glutamyltranspeptidase (Ggt) Small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1663
Polymers60,9882
Non-polymers1791
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11390 Å2
ΔGint-65 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.711, 105.376, 91.927
Angle α, β, γ (deg.)90.00, 91.69, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe enzyme is a heterotetramer generated by the autocatalytic cleavage of the proenzyme.

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Components

#1: Protein Gamma-glutamyltranspeptidase (Ggt) Large subunit


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) Small subunit


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-AVN / (2S)-AMINO[(5S)-3-CHLORO-4,5-DIHYDROISOXAZOL-5-YL]ACETIC ACID / ACIVICIN / Acivicin


Type: L-peptide linking / Mass: 178.574 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H7ClN2O3 / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 43.36 %
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: 1.7→50 Å / Num. obs: 110177 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 23.306
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.641 / % possible all: 95.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å26.47 Å
Translation2.5 Å26.47 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
SOLOMONphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→29.2 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.588 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21087 10906 9.9 %RANDOM
Rwork0.17789 ---
obs0.18116 99222 96.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.176 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å21.11 Å2
2---1.35 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8086 0 20 534 8640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228310
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.51.97111236
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.33951074
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69125.285333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.591151449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7671528
X-RAY DIFFRACTIONr_chiral_restr0.0980.21256
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026214
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.24181
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.25811
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2595
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7941.55453
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16228522
X-RAY DIFFRACTIONr_scbond_it2.06633228
X-RAY DIFFRACTIONr_scangle_it3.0514.52714
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 720 -
Rwork0.236 7106 -
obs--93.53 %
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)
11.1878-0.12820.50361.2153-0.33611.58110.03640.0309-0.2859-0.14850.09760.08710.2896-0.2733-0.1340.0062-0.0667-0.0550.1654-0.0353-0.003435.283-14.88130.949
20.7225-0.5865-0.03061.38280.28351.8699-0.0461-0.0675-0.0837-0.04430.1494-0.19510.09910.23-0.1034-0.006-0.0167-0.04040.1746-0.04170.019950.421-12.99339.623
30.5417-0.15810.04220.8262-0.27661.2302-0.0524-0.0522-0.07070.0720.0988-0.0085-0.0531-0.0301-0.0465-0.0106-0.0151-0.05980.1643-0.0231-0.059942.274-3.93939.555
42.07231.5822-1.12873.61790.51464.9675-0.06740.03170.3312-0.07690.01550.2937-0.8891-0.49930.05190.27220.0361-0.10470.1936-0.0410.023739.87524.40237.586
50.2313-0.4527-0.1470.9593-0.07951.93510.0009-0.1443-0.13580.02330.0918-0.09710.04070.0185-0.09280.0122-0.0177-0.03850.1871-0.04160.031645.013-9.44338.072
60.61520.02990.0830.7511-0.47671.3336-0.05950.0491-0.02570.02840.0832-0.0011-0.204-0.0956-0.02380.0606-0.0185-0.04430.1824-0.0284-0.044240.4156.27529.581
71.63662.5958-0.21084.88811.90186.5144-0.23310.9392-0.1691-0.18710.48740.22830.157-0.2946-0.25440.1948-0.009-0.06480.1799-0.00690.158432.585-6.36720.657
81.09350.2971-0.27871.336-0.15481.4676-0.04370.0631-0.1666-0.15010.0104-0.02810.10880.13270.03330.02560.0158-0.02740.13460.00820.006840.646-8.601-14.89
91.36920.5937-0.65922.2398-0.52012.3834-0.09940.1319-0.0891-0.1970.11480.22010.2866-0.2479-0.01540.0078-0.0403-0.07350.0973-0.00830.013526.093-15.157-14.914
100.6320.0417-0.14571.03560.2080.91370.0025-0.00710.0715-0.16970.0713-0.151-0.23260.209-0.07370.0281-0.0443-0.02650.16110.0113-0.032647.77115.336-11.232
1117.46627.68378.27478.0942-13.114563.4707-0.79140.52710.6178-0.94420.05230.26352.6617-1.27790.7390.2579-0.0021-0.00040.25880.0050.260747.32524.583-26.389
120.80680.3033-0.30661.2045-0.08641.1028-0.02940.0521-0.0572-0.1740.03330.0204-0.0680.0075-0.00390.03060.0075-0.05130.13060.0087-0.026236.688-0.173-16.068
130.9681-0.2016-0.15071.41890.31150.8247-0.0142-0.1007-0.03790.08920.0444-0.0492-0.08140.1513-0.03020.0186-0.0098-0.05210.1950.0222-0.03143.2049.2891.477
149.6917-4.7338-0.02532.9537-0.39623.1739-0.2354-0.6927-0.26170.0660.2634-0.09260.15650.2861-0.0280.0452-0.0044-0.04340.19080.08420.156746.97-4.872.937
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 104
2X-RAY DIFFRACTION2A105 - 188
3X-RAY DIFFRACTION3A189 - 354
4X-RAY DIFFRACTION4A355 - 372
5X-RAY DIFFRACTION5B381 - 428
6X-RAY DIFFRACTION6B429 - 548
7X-RAY DIFFRACTION7B549 - 567
8X-RAY DIFFRACTION8C32 - 162
9X-RAY DIFFRACTION9C163 - 256
10X-RAY DIFFRACTION10C257 - 372
11X-RAY DIFFRACTION11C373 - 379
12X-RAY DIFFRACTION12D381 - 458
13X-RAY DIFFRACTION13D459 - 551
14X-RAY DIFFRACTION14D552 - 567

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