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- PDB-8xtf: Crystal structure of methyltransferase MpaG' in complex with SAH ... -

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Basic information

Entry
Database: PDB / ID: 8xtf
TitleCrystal structure of methyltransferase MpaG' in complex with SAH and FDHMP-3C
ComponentsO-methyltransferase mpaG'
KeywordsBIOSYNTHETIC PROTEIN / methyltransferase / MpaG' / MPA biosynthesis
Function / homology
Function and homology information


mycophenolic acid biosynthetic process / polyketide synthase activity / terpenoid biosynthetic process / O-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / cytosol
Similarity search - Function
O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / N-6 Adenine-specific DNA methylases signature. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
: / S-ADENOSYL-L-HOMOCYSTEINE / O-methyltransferase mpaG'
Similarity search - Component
Biological speciesPenicillium brevicompactum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsYou, C. / Pan, Y.J. / Li, S.Y. / Feng, Y.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070125 China
CitationJournal: Protein Sci. / Year: 2024
Title: Structural basis for substrate flexibility of the O-methyltransferase MpaG' involved in mycophenolic acid biosynthesis.
Authors: You, C. / Pan, Y. / Liu, R. / Li, S. / Feng, Y.
History
DepositionJan 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: O-methyltransferase mpaG'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4523
Polymers43,6931
Non-polymers7592
Water3,315184
1
A: O-methyltransferase mpaG'
hetero molecules

A: O-methyltransferase mpaG'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9046
Polymers87,3862
Non-polymers1,5184
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_444x-y-1/3,-y-2/3,-z-2/31
Buried area8890 Å2
ΔGint-73 kcal/mol
Surface area29710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)211.754, 211.754, 67.424
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"

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Components

#1: Protein O-methyltransferase mpaG' / Mycophenolic acid biosynthesis cluster protein G'


Mass: 43693.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium brevicompactum (fungus) / Strain: NRRL 864 / Gene: mpaG' / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0B5L781, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-A1LWC / 4-farnesyl-3,5-dihydroxy-6-methylphthalide-3C / (4~{E},8~{E})-4,8-dimethyl-10-[7-methyl-4,6-bis(oxidanyl)-3-oxidanylidene-1~{H}-2-benzofuran-5-yl]deca-4,8-dienoic acid


Mass: 374.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H26O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 3.33 Å3/Da / Density % sol: 63.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 10%PEG 8000, 0.1 M CHES, pH 9.5 and 0.2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.13→63.36 Å / Num. obs: 32213 / % possible obs: 100 % / Redundancy: 2 % / Biso Wilson estimate: 23.33 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.074 / Rrim(I) all: 0.105 / Χ2: 0.5 / Net I/σ(I): 6.2
Reflection shellResolution: 2.13→2.19 Å / % possible obs: 99.9 % / Redundancy: 2 % / Rmerge(I) obs: 0.433 / Num. measured all: 5160 / Num. unique obs: 2619 / CC1/2: 0.614 / Rpim(I) all: 0.433 / Rrim(I) all: 0.612 / Χ2: 0.51 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.13→37.91 Å / SU ML: 0.2464 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6239
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2101 1558 4.84 %RANDOM
Rwork0.1691 30627 --
obs0.1711 32185 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.71 Å2
Refinement stepCycle: LAST / Resolution: 2.13→37.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3053 0 53 184 3290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00733181
X-RAY DIFFRACTIONf_angle_d0.83224327
X-RAY DIFFRACTIONf_chiral_restr0.0501471
X-RAY DIFFRACTIONf_plane_restr0.0063569
X-RAY DIFFRACTIONf_dihedral_angle_d5.9573464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.20.28961420.23082760X-RAY DIFFRACTION99.73
2.2-2.280.25811470.21062763X-RAY DIFFRACTION99.86
2.28-2.370.26171570.20982756X-RAY DIFFRACTION99.86
2.37-2.480.2431370.19822762X-RAY DIFFRACTION99.9
2.48-2.610.26681530.19772760X-RAY DIFFRACTION99.86
2.61-2.770.24081540.19392764X-RAY DIFFRACTION99.97
2.77-2.990.27611420.19172772X-RAY DIFFRACTION100
2.99-3.290.21271160.17962803X-RAY DIFFRACTION100
3.29-3.760.19281420.15972806X-RAY DIFFRACTION100
3.76-4.740.1391390.12492814X-RAY DIFFRACTION100
4.74-37.910.15271290.13452867X-RAY DIFFRACTION99.7
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)
12.97859908276-0.9959984471860.1878305698863.242538163770.9725526984971.68122495014-0.151013677439-0.0931274672402-0.004312512755070.542057642888-0.1104027608560.7323968917140.0151916189637-0.5411449591330.2217449467170.251069375450.01023288769240.04438727760490.385343081847-0.09396092621350.349298446067-19.3923857536-58.4277313286-16.9671356544
20.8311445425270.287219594643-0.09740610731122.23949321275-0.2945244796291.72751174306-0.01033258236630.1321186084890.0927718551059-0.271371866128-0.002140557929710.00267383051305-0.252706258439-0.0696453071903-0.006315631893680.225581960750.03196770368520.004222457910410.143806169987-0.008059503821840.1171311415211.11642489707-54.8430770406-35.5935491201
31.4927390859-0.3801675492530.3675959023731.4604248636-0.4789545354031.883072013160.04853103515830.1947456233460.046307556521-0.22688092906-0.09200636827640.114603079687-0.0868782645705-0.03106434634210.05708185071420.2423952104780.0310257846227-0.008358838036270.161036794343-0.02767303040260.147973886956-0.46773191962-48.4332707257-30.7529795989
41.795322354050.543580842586-0.4374285433983.58195213833-1.31746828160.7120662533020.126251193158-0.173070365196-0.02924611160270.393008069465-0.168984790947-0.4683445988720.1048357108650.08105369845440.02979709220860.264941054462-0.00273291582127-0.04671905824050.217150972944-0.03652693425030.25456450784616.3554655349-59.7389531918-9.44545113098
51.26715792076-0.611924725919-0.8013662293471.03972418750.6613540172361.448950642410.01905906213030.06837704615730.00113540110341-0.0259376311129-0.04290783896090.0272502049766-0.0554528828926-0.1172942034670.01811435697220.162884186634-0.0119756205317-0.006399837305860.154978256171-0.002510747297040.2089106283060.469180298915-35.9421698258-8.37976369342
64.91257995349-0.985708799364-2.058598941091.209561997891.230779034842.157677355530.2797722625080.3244204072740.40511510528-0.184359382525-0.0486192911714-0.217128269477-0.375010908342-0.0155384211647-0.2202808284880.1935856998130.001772350302740.01504629675790.1624595580540.03222695363930.2198426789044.65292474379-26.9431094559-10.1538844511
71.62910049368-0.07171209325530.01222505477611.871984297380.5326291953161.32276272483-0.0958237568253-0.0950211108435-0.03884740750350.07520725368510.0850924884625-0.03737976499280.08884798341180.0745727091566-0.005461607820080.163849415029-0.00268493016164-0.01543299699060.165755917329-0.01036498386510.1822654901534.7381618126-37.0970460723.67889212989
80.455995489527-0.473540164413-0.255399152241.527124355620.4889638311963.12749631816-0.02188032853530.0536537119506-0.1317985560780.03289386579480.0775551748546-0.0528246476190.0656893202046-0.132341726487-0.06813171178760.255164296668-0.03252264740070.01427055588610.210723228729-0.02386242182680.2022123686920.765051139034-53.2955645267-1.0705321908
93.33972747660.2989982525010.7540999890672.235477766510.3304439763151.142463250920.00275094613345-0.149292862941-0.05180769020250.112978132453-0.1225363291990.1994786973350.18111436969-0.4386833579280.1041488201380.18031984082-0.05078610795770.01942334116870.186337665866-0.02150246245290.182998442383-7.1878052977-42.47606746873.46172700195
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 42 )4 - 421 - 39
22chain 'A' and (resid 43 through 108 )43 - 10840 - 105
33chain 'A' and (resid 109 through 143 )109 - 143106 - 140
44chain 'A' and (resid 144 through 181 )144 - 181141 - 178
55chain 'A' and (resid 182 through 252 )182 - 252179 - 249
66chain 'A' and (resid 253 through 284 )253 - 284250 - 281
77chain 'A' and (resid 285 through 336 )285 - 336282 - 333
88chain 'A' and (resid 337 through 375 )337 - 375334 - 372
99chain 'A' and (resid 376 through 398 )376 - 398373 - 395

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