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- PDB-7d9w: Gamma-glutamyltranspeptidase from Pseudomonas nitroreducens compl... -

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Basic information

Entry
Database: PDB / ID: 7d9w
TitleGamma-glutamyltranspeptidase from Pseudomonas nitroreducens complexed with L-DON
Components(Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03) x 2
KeywordsTRANSFERASE / theanine synthesis / transpeptidation / enzyme / protein engineering / substrate specificity / reaction specificity
Function / homology
Function and homology information


hypoglycin A gamma-glutamyl transpeptidase activity / glutathione hydrolase activity / leukotriene C4 gamma-glutamyl transferase activity / glutathione catabolic process
Similarity search - Function
Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase signature. / Gamma-glutamyltranspeptidase, large subunit, C-terminal domain / Gamma-glutamyltranspeptidase, small subunit / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
6-DIAZENYL-5-OXO-L-NORLEUCINE / GLYCINE / Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03
Similarity search - Component
Biological speciesPseudomonas nitroreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHibi, T. / Sano, C. / Putthapong, P. / Hayashi, J. / Itoh, T. / Wakayama, M.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Mutagenesis and structure-based analysis of the role of Tryptophan525 of gamma-glutamyltranspeptidase from Pseudomonas nitroreducens.
Authors: Sano, C. / Itoh, T. / Phumsombat, P. / Hayashi, J. / Wakayama, M. / Hibi, T.
#1: Journal: Biosci Biotechnol Biochem / Year: 2019
Title: Crystal structure analysis and enzymatic characterization of gamma-glutamyltranspeptidase from Pseudomonas nitroreducens.
Authors: Hibi, T. / Imaoka, M. / Shimizu, Y. / Itoh, T. / Wakayama, M.
History
DepositionOct 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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-glutamyltransferase 1 Threonine peptidase. MEROPS family T03
B: Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03
C: Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03
D: Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,7158
Polymers122,2194
Non-polymers4964
Water7,674426
1
A: Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03
B: Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3574
Polymers61,1092
Non-polymers2482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11440 Å2
ΔGint-79 kcal/mol
Surface area17540 Å2
MethodPISA
2
C: Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03
D: Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3574
Polymers61,1092
Non-polymers2482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11470 Å2
ΔGint-76 kcal/mol
Surface area17860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.516, 53.846, 107.549
Angle α, β, γ (deg.)91.590, 100.314, 108.058
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03


Mass: 40283.793 Da / Num. of mol.: 2 / Fragment: L-subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas nitroreducens (bacteria) / Gene: SAMN05216209_3923 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A239KXH0
#2: Protein Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03


Mass: 20825.461 Da / Num. of mol.: 2 / Fragment: S-subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas nitroreducens (bacteria) / Gene: SAMN05216209_3923 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A239KXH0
#3: Chemical ChemComp-DON / 6-DIAZENYL-5-OXO-L-NORLEUCINE / (S)-2-AMINO-6-DIAZENYL-5-OXOHEXANOIC ACID


Type: L-peptide linking / Mass: 173.170 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H11N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.95 Å3/Da / Density % sol: 37.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 16% PEG 8000, 15% PE G400, 0.1M HEPES pH 7, 25mM L-DON,25mM DON, 80 mM Gly, gamma-butyllactone

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40.56 Å / Num. obs: 68628 / % possible obs: 97.7 % / Redundancy: 7.1 % / Biso Wilson estimate: 25.42 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 16
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.628 / Num. unique obs: 3389 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZJG

5zjg


Resolution: 1.9→40.56 Å / SU ML: 0.1518 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 20.1405
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1822 1998 2.91 %
Rwork0.1561 66581 -
obs0.1569 68579 95.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.58 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7766 0 28 426 8220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00418023
X-RAY DIFFRACTIONf_angle_d0.817110924
X-RAY DIFFRACTIONf_chiral_restr0.04761225
X-RAY DIFFRACTIONf_plane_restr0.00491438
X-RAY DIFFRACTIONf_dihedral_angle_d13.95862788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.23071000.20813321X-RAY DIFFRACTION67.5
1.95-20.25041460.19234870X-RAY DIFFRACTION96.59
2-2.060.22741450.18254817X-RAY DIFFRACTION96.82
2.06-2.120.22891430.18144766X-RAY DIFFRACTION96.82
2.12-2.20.21181450.17564836X-RAY DIFFRACTION97.13
2.2-2.290.22191470.15894877X-RAY DIFFRACTION97.18
2.29-2.390.18191430.15394815X-RAY DIFFRACTION97.44
2.39-2.520.19851460.15974870X-RAY DIFFRACTION97.64
2.52-2.680.19351450.15424834X-RAY DIFFRACTION97.88
2.68-2.880.17111470.15554919X-RAY DIFFRACTION98.01
2.88-3.170.17911470.15464864X-RAY DIFFRACTION98.37
3.17-3.630.16921480.15524945X-RAY DIFFRACTION98.78
3.63-4.580.14941470.12944911X-RAY DIFFRACTION99.06
4.58-40.560.17231490.15924936X-RAY DIFFRACTION99.14
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)
11.44848636851-0.861905792228-0.4843637318751.950723607850.4387895110321.1639876471-0.20173286252-0.2490028541690.01370598614240.3373484089760.212668356085-0.07114422815910.05507624850150.0498123965138-0.005807943085630.2417422722970.1479248951890.007318274207480.297940351293-0.007434973047040.209618573298-8.4131269639-27.7747288655105.947766969
22.20433590984-1.078208214681.318003837912.70515614867-0.1023874308330.941774920725-0.176960531221-0.2108009565010.3062255820780.0635453357960.362335908576-1.183404121360.2781972755150.7218876240950.06339677142350.2579533398920.1402617638350.01122950211850.507682843502-0.1831272063130.62122419825410.7268800668-22.6043124273104.622077751
31.63490924681-0.789612402519-0.2661032697862.318424315410.7785636857181.3786496014-0.103656499398-0.1183075147560.1305540195310.2604397211770.1575117970660.0110910073019-0.00945623969750.0238408112597-0.04415694527690.2290549301550.1377023579090.03512610846920.2808496806680.005984155216510.205698594714-12.6832382635-22.3730534354104.390523951
40.91737587818-0.376422571233-0.4293513559061.42488608050.9486707442411.536360986890.02873900098910.192706079612-0.0286597994601-0.234304527804-0.2198657643630.181501121323-0.105872691864-0.3585214338170.1366450870260.2449362749810.07863150323930.004246331681180.288837149899-0.01320602648460.227785678154-12.7014036091-40.942252833378.9474320212
51.77353108756-0.8510571499550.001745127390113.875223257440.1932209403230.615572051782-0.0312817858771-0.01349828274010.133846947887-0.05874467802330.0984805553749-0.1490111520840.02933839898310.062522153117-0.02978585142280.2132983692880.117518927120.03158012281380.275626866244-0.02668092611930.228565130764-5.20757826523-26.686060814698.3713050683
61.71476444661-1.7656893245-0.1441338925415.84323771526-0.8157235282131.85605643818-0.01876481184870.0956333819968-0.139524501872-0.118506180538-0.06744540813430.4091338289930.0674264670174-0.1748293325520.07512669089820.1718858879580.08345779260710.02749438505380.260990177152-0.03154978735750.211300998104-13.2263366093-33.616613325494.6618824724
71.270700767080.33129372298-0.5157947856822.03450796697-0.3072539502333.0770203999-0.04978005360760.007989029989850.0489697564764-0.05610780703780.05632385340260.0338036431410.12763843850.1185779653910.009440465049670.1861050777110.09390286358210.03965155512750.1956449944830.006518695568720.205062273463-0.716777267689-43.702492279187.6999560958
81.64956984448-0.486361729292-0.862116629381.464078674260.2102741813154.49772175601-0.101705079831-0.0599939485225-0.03232975697920.1095119270080.148766873539-0.06814819461970.07495568550760.2754965754690.04096061814840.1820216180770.08029214482570.04335339919050.2009865196290.03311318982580.2515975340851.91125408107-44.38006929689.7190826671
93.20776983845-0.8116366219710.1646206055952.266621190761.334565571521.2772882578-0.271474669441-0.717736960354-0.2472856090650.4644428358080.3290661399360.1103844236130.4471139282920.496109541651-0.1075334102230.4153386180120.2629400016910.02284528168030.4393513095690.02759029472060.3219358040821.13606203163-43.7090841343107.873223578
101.23659104388-0.0276531201675-0.115250653572.176750723611.232265173513.364670461530.0388400744871-0.139535141991-0.02685021146190.03343169027540.106382360376-0.1023962083650.2094587613590.263192722611-0.1469620054250.1915076583620.08103626795760.02567637445290.2070267088850.02271394828680.164849994062-5.64767729734-11.794717267554.7366467478
111.05785330987-1.04228211406-0.02048173683664.515119268921.838760498964.28387253214-0.0231967651354-0.251600349425-0.243814866262-0.0527510313928-0.218506813620.7759936572680.410729097106-1.169658702370.2302822008190.275035395801-0.1234514805380.02349162689540.5053230482840.0252791909490.370512964173-24.5484996047-17.263688749357.6921436661
121.201818594-0.0357275703278-0.4836332521061.840547940050.1260248033543.571919101830.0144451189942-0.125526131434-0.1184531529430.01187391585090.0892886015021-0.2575583941460.5095088997810.402832614012-0.09676696677320.3193108823890.1282672434030.001761732558720.279289888157-0.01437529390540.221726461553-1.80494349028-17.708341613352.4741571617
131.05577285847-0.137416857243-0.2639108955080.3393632770890.4318129976582.17772788520.2770113428710.2877816309260.0665085504336-0.650779203065-0.244687342155-0.0606552757984-0.3891836206670.0556972042728-0.01966814771470.6184378441660.15108625280.07747475569870.33013768620.002342987034590.225761263119-6.67884081106-1.1653544806125.8948800721
141.317159376810.0542033282839-0.01152710750292.389416689640.5384833892452.90015082390.1069875509050.0640310592823-0.0801746558403-0.284902624961-0.0162678783194-0.01059435915430.0657539316180.129084021757-0.08315646621330.238534017950.0815742551950.03119502396770.1770978501010.01948266506190.173669683242-7.61946350224-11.270569785545.548134558
151.30589431572-0.34526495567-0.226180042150.8429642541170.3011489909761.797247782870.08092085965840.179863148916-0.0503147153136-0.272607296695-0.1310904391720.30827506225-0.474501280292-0.4021078590850.06594918037250.4799759286410.187801510926-0.01212628601750.291688962746-0.01799867981310.260132549762-19.32786379531.7284314904835.7433272594
164.94674016511.410091868210.7685341889763.129711710540.8221686923222.586052731380.06857308298-0.3539733037590.417219632043-0.09505840975460.00480871329611-0.0251525268898-0.851394714954-0.0668219845952-0.08787276627310.4456083943820.1029033911090.09299797657340.26292568772-0.03672469414950.248686396496-11.25929067757.0638569173155.4590968896
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 26 through 159 )AA26 - 1591 - 135
22chain 'A' and (resid 160 through 199 )AA160 - 199136 - 175
33chain 'A' and (resid 200 through 270 )AA200 - 270176 - 246
44chain 'A' and (resid 271 through 360 )AA271 - 360247 - 336
55chain 'B' and (resid 364 through 421 )BC364 - 4211 - 59
66chain 'B' and (resid 422 through 456 )BC422 - 45660 - 94
77chain 'B' and (resid 457 through 506 )BC457 - 50695 - 144
88chain 'B' and (resid 507 through 544 )BC507 - 544145 - 182
99chain 'B' and (resid 545 through 557 )BC545 - 557183 - 195
1010chain 'C' and (resid 26 through 159 )CF26 - 1591 - 135
1111chain 'C' and (resid 160 through 199 )CF160 - 199136 - 175
1212chain 'C' and (resid 200 through 270 )CF200 - 270176 - 246
1313chain 'C' and (resid 271 through 363 )CF271 - 363247 - 339
1414chain 'D' and (resid 364 through 456 )DH364 - 4561 - 94
1515chain 'D' and (resid 457 through 530 )DH457 - 53095 - 168
1616chain 'D' and (resid 531 through 557 )DH531 - 557169 - 196

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