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- PDB-7d9x: Highly active mutant W525D of Gamma-glutamyltranspeptidase from P... -

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Basic information

Entry
Database: PDB / ID: 7d9x
TitleHighly active mutant W525D of Gamma-glutamyltranspeptidase from Pseudomonas nitroreducens
Components(Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family ...) 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
GAMMA-BUTYROLACTONE / GLYCINE / Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03
Similarity search - Component
Biological speciesPseudomonas nitroreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsHibi, T. / Sano, C. / 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)122,81913
Polymers122,0764
Non-polymers7439
Water16,502916
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)61,4537
Polymers61,0382
Non-polymers4145
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12420 Å2
ΔGint-76 kcal/mol
Surface area17920 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)61,3666
Polymers61,0382
Non-polymers3284
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12140 Å2
ΔGint-75 kcal/mol
Surface area18140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.624, 117.189, 187.589
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family ... , 2 types, 4 molecules ACBD

#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: 20754.340 Da / Num. of mol.: 2 / Fragment: S-subunit / Mutation: W525D
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

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Non-polymers , 4 types, 925 molecules

#3: Chemical ChemComp-GBL / GAMMA-BUTYROLACTONE / DIHYDROFURAN-2(3H)-ONE


Mass: 86.089 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O2
#4: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 916 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 16% PEG 8000, 15% PEG 400, 0.1M HEPES pH 7, 50mM Gly-Gly

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.74→46.9 Å / Num. obs: 111797 / % possible obs: 99.5 % / Redundancy: 13.8 % / Biso Wilson estimate: 24.67 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 47.9
Reflection shellResolution: 1.74→1.79 Å / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 5485 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZJG

5zjg


Resolution: 1.74→46.9 Å / SU ML: 0.1473 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.8681
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.187 1997 1.79 %
Rwork0.1669 109629 -
obs0.1673 111626 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.12 Å2
Refinement stepCycle: LAST / Resolution: 1.74→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7851 0 50 916 8817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00778136
X-RAY DIFFRACTIONf_angle_d0.846911060
X-RAY DIFFRACTIONf_chiral_restr0.05391225
X-RAY DIFFRACTIONf_plane_restr0.00541460
X-RAY DIFFRACTIONf_dihedral_angle_d14.7632875
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.790.25481340.23097356X-RAY DIFFRACTION94.34
1.79-1.840.27911420.22477774X-RAY DIFFRACTION99.75
1.84-1.890.25381410.21687746X-RAY DIFFRACTION99.82
1.89-1.950.23691410.19777768X-RAY DIFFRACTION99.9
1.95-2.020.19211430.18697835X-RAY DIFFRACTION99.91
2.02-2.10.21611420.18517778X-RAY DIFFRACTION99.97
2.1-2.20.20031420.17577802X-RAY DIFFRACTION99.96
2.2-2.310.2081430.16517825X-RAY DIFFRACTION99.82
2.31-2.460.17731430.1657857X-RAY DIFFRACTION99.83
2.46-2.650.18581440.16537837X-RAY DIFFRACTION99.66
2.65-2.910.19551420.16547892X-RAY DIFFRACTION99.52
2.91-3.340.19371430.16597908X-RAY DIFFRACTION99.59
3.34-4.20.18211470.14757979X-RAY DIFFRACTION99.73
4.2-46.90.14671500.15638272X-RAY DIFFRACTION99.29
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)
10.8685776942590.1572266474680.2710560364480.986910231225-0.531367467061.637940874530.001541553451320.0523784134197-0.00950530228025-0.1570310366810.05840014690.0283080384809-0.0405816513508-0.0431566688361-0.06660718670430.2468815912430.02226917533660.0011410560280.1894915242680.01215458694050.204868714871.38441480348-14.0595808158-32.0773486807
21.162476992050.1018485797550.4864221289311.52277967333-0.6220452275022.763075449680.04426406601390.119585821414-0.0977941234949-0.2226598729180.0616396704304-0.0504068501666-0.02499218569140.101444452755-0.121098624570.2304517886410.02740868088570.01429413147910.188751714708-0.01961346930810.1989095992323.7200873599-19.5899082273-35.7921762799
31.004438854510.1537605218370.1415416913951.48086664147-1.063508233912.88959116965-0.02890411122890.01634273184520.10817182061-0.199899632330.1299130134350.314114727041-0.478218992918-0.611071270926-0.0825535738220.4026631401360.0705217171946-0.09064554159920.3484932575490.03269631928750.388223989397-15.313179882-15.6699679389-37.4299809567
40.817431353152-0.3527242784720.9535578651512.43095815925-0.9120402861382.121739053110.0159982365954-0.0777458668088-0.165846976712-0.4473754566860.2598683695570.4724046008990.118480262086-0.426142380513-0.2171092131080.350177089111-0.00764970554285-0.1269869600870.3782907821610.04122326281860.344335139971-16.623669611-19.2093357939-43.3139995148
51.908873335440.3384769241640.2081471869141.15575181351-0.4293147201142.995094792790.08531767292640.242916207262-0.317307425366-0.5871359894540.0853646569011-0.003555999998730.2853762502110.106574076346-0.1693709238250.3893389861630.0334512461838-0.05997357279630.22459186765-0.06006854022780.302030641429-0.169505303939-28.8320477748-41.9324142809
60.9310000344790.2919817848310.7987623233221.01521937661-0.4832481845621.43220546693-0.1153463623120.07788294689720.152479346815-0.1345435835210.060312840304-0.245549496524-0.6529467307650.3168276477710.05314721471260.395440313843-0.07367914406080.01998045279880.2103563178530.02451903929180.1862976485689.73865497951-0.145951936167-30.376758396
70.809346770306-0.004931534415870.0461811572241.27424857421-0.1651244329481.06225102843-0.1609276302190.1473209104470.368799584716-0.2156406650490.0815308180028-0.223637473242-0.7948804665630.06095611540890.03050136745150.850003281932-0.106334661786-0.05035605120090.2480143923450.07177224033920.292834107056.3922689619412.8918996786-35.9922647976
80.272459334349-0.3632724047620.2399831344331.54531285786-0.1463861021930.311761416887-0.02241505154870.2043478810980.322962194836-0.422349999278-0.102971193588-0.378925148719-1.0101617780.5124598403930.1790791468770.848015372171-0.2968542107840.02320223962880.350166100380.1015643352050.32813557933315.675044271610.701464365-37.7088414555
90.9863565087670.002382423605130.3907094890051.324306962530.03292394087691.92564335289-0.01800824520250.1963446074310.0685434650894-0.3404393603370.0524543033322-0.10907168048-0.3612083291940.242381539588-0.04540921618210.340794168941-0.0005944815659920.02856030919770.219686021940.02203932689710.2026571788133.13288904468-8.57528026386-37.6774445539
101.325399738560.544481055571-0.1348157003531.95934592062-0.3929663712270.911569117629-0.2245384236780.06295410458210.289634747102-0.3098059327060.1256935362390.232057479528-0.839496511209-0.275205127269-0.008465231242040.6409361504180.11057571226-0.08119770157990.23295765530.02555014002030.253200830635-4.118611323038.38295428198-30.8435355132
112.845275878870.2496942838361.763638355231.141529551110.09843255792283.97543402764-0.0562094422677-0.39579980644-0.03522237976710.2162347214030.1018454910780.110456346406-0.368133991576-0.470661311828-0.04516971017140.2942631812520.1092985426050.04613292426310.3058412983090.01681386433270.22260721119-6.40261436649-6.58384823166-17.250287883
122.093287449490.248558390235-0.1513701970192.68386773421-0.01008894073552.461347889610.05680679963730.1258628933260.270307884709-0.175925727961-0.0209643125898-0.127574528774-0.2708289469920.0393346562578-0.03003365098520.175890763902-0.00423132734021-0.01222744462510.1919893010990.006484363394210.213177220674-9.8396482291121.1164327946-88.5014902686
130.911335984021-0.2758164362170.2531539390422.056379440280.5316134898621.33474805810.0350415634503-0.125259604806-0.08134368000080.3448603211870.0408928322957-0.05907475956650.142673118799-0.0487049646459-0.05250162976310.123263453531-0.0144239564883-0.039578300660.200349676941-0.01006312398890.169757040386-13.26937078136.49634004071-73.2369479968
140.562278032989-0.857369922082-0.09921865214791.51080494574-0.2012721737681.453853956610.0322231342184-0.17342022057-0.07978986496940.479857494981-0.00139541267838-0.158094834440.0197286591749-0.0557561058101-0.01523790622920.149470557638-0.00607464323218-0.02405334571340.231620899036-0.01965106253460.159393475345-13.954686981310.8957082379-69.8461231424
151.883970270530.0664727006060.289166331211.66990427940.2684868583211.13439668889-0.00181170499695-0.05371447565770.007364118549490.129029002967-0.0914933738960.305582657538-0.107584396505-0.314102079360.05532543846980.1111095670150.009775220014840.02208945266230.270511229901-0.06269829045850.238677949302-27.130370439915.5315533481-76.245187794
161.00637927378-0.299447228524-0.3419471854062.310384370070.64306821611.692095298350.0352169168962-0.2513622301440.012879213750.4960976980440.0499141929912-0.1928813310140.1311797470310.0937920089289-0.07046138463810.207826413988-0.0205751562575-0.07698449600450.2338015371570.001456898512050.190966259457-9.975358326695.58444738831-69.6638043175
171.86841637516-0.44045589590.8713978648211.50925448077-0.07269738920252.361471648210.1487685289920.241584204281-0.193417439413-0.251964814898-0.0272557142004-0.4259506373270.2608865160630.265889991003-0.1332183655220.2401195260520.04404984623560.01976292933830.243228241164-0.05434532783340.3660645491-1.19820974752-11.4962721785-93.6111545074
181.37484015796-0.1353184343840.7647320111131.51415999524-0.3806858321963.189791607080.0841915648774-0.079501168453-0.3115998133270.02547423900470.0584230351111-0.2106581104680.4970246718930.0227557892214-0.1587572618990.2631741363820.0160108544667-0.08122315000380.2017114608330.001538664974610.393897504167-7.27232100925-15.4067817559-86.4448165803
191.266199711210.03023145269350.5978292290281.500979226010.5480211257851.879808788390.179298432995-0.0948813182242-0.4793871886910.2612326599590.0561248601257-0.3930274964640.4426681544050.161793924761-0.2228399543860.3255074653080.0461664164391-0.1259056489750.2381959671950.01628452363450.471583023099-1.15744258806-16.8459194617-78.9499794486
201.16679234877-0.0930189445799-0.1254366687471.542204682340.4943884423771.897871069870.0609813770924-0.145773144898-0.1436967351780.284847899833-0.05449122818530.02417919583710.312232219985-0.0926541627599-0.02040657970190.17655004319-0.0189701127273-0.03622412058260.21661394674-0.0001688342437760.193743624727-16.26946082072.22792516891-74.3914610672
210.9529080619450.09863705448030.3968534579091.992650260250.378864222281.274824023460.03771705157150.0897886810756-0.157219546789-0.2055236092780.0349829359691-0.09072152454010.1385018316960.00964164824836-0.07186705135980.1416219869830.00334787014218-0.01780862842570.199203868003-0.01368689200370.208833766199-11.4085774605-1.87759145063-92.1768917742
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 113 )AA26 - 1131 - 89
22chain 'A' and (resid 114 through 150 )AA114 - 15090 - 126
33chain 'A' and (resid 151 through 178 )AA151 - 178127 - 154
44chain 'A' and (resid 179 through 199 )AA179 - 199155 - 175
55chain 'A' and (resid 200 through 233 )AA200 - 233176 - 209
66chain 'A' and (resid 234 through 296 )AA234 - 296210 - 272
77chain 'A' and (resid 297 through 317 )AA297 - 317273 - 293
88chain 'A' and (resid 318 through 361 )AA318 - 361294 - 337
99chain 'B' and (resid 364 through 446 )BD364 - 4461 - 84
1010chain 'B' and (resid 447 through 530 )BD447 - 53085 - 168
1111chain 'B' and (resid 531 through 557 )BD531 - 557169 - 195
1212chain 'C' and (resid 26 through 52 )CI26 - 521 - 27
1313chain 'C' and (resid 53 through 113 )CI53 - 11328 - 89
1414chain 'C' and (resid 114 through 146 )CI114 - 14690 - 122
1515chain 'C' and (resid 147 through 219 )CI147 - 219123 - 195
1616chain 'C' and (resid 220 through 270 )CI220 - 270196 - 246
1717chain 'C' and (resid 271 through 296 )CI271 - 296247 - 272
1818chain 'C' and (resid 297 through 317 )CI297 - 317273 - 293
1919chain 'C' and (resid 318 through 361 )CI318 - 361294 - 337
2020chain 'D' and (resid 364 through 431 )DL364 - 4311 - 69
2121chain 'D' and (resid 432 through 557 )DL432 - 55770 - 196

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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