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- PDB-8cxz: CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA... -

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Basic information

Entry
Database: PDB / ID: 8cxz
TitleCamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Inhibitor N6-(3-Phenylpropyl)adenosine (Compound 14)
Components
  • (DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)- ...) x 2
  • Site-specific DNA-methyltransferase (adenine-specific)
KeywordsDNA BINDING PROTEIN/DNA / DNA Adenine Methylation / PROTEIN-DNA COMPLEX / TRANSFERASE / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA modification / methylation / nucleic acid binding / hydrolase activity
Similarity search - Function
TaqI-like C-terminal specificity domain / TaqI-like C-terminal specificity domain / Type II restriction enzyme and methyltransferase RM.Eco57I-like / Eco57I restriction-modification methylase / : / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
: / N-(3-phenylpropyl)adenosine / DNA / DNA (> 10) / site-specific DNA-methyltransferase (adenine-specific)
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.35 Å
AuthorsZhou, J. / Horton, J.R. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
CitationJournal: J.Med.Chem. / Year: 2023
Title: Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence.
Authors: Zhou, J. / Horton, J.R. / Menna, M. / Fiorentino, F. / Ren, R. / Yu, D. / Hajian, T. / Vedadi, M. / Mazzoccanti, G. / Ciogli, A. / Weinhold, E. / Huben, M. / Blumenthal, R.M. / Zhang, X. / ...Authors: Zhou, J. / Horton, J.R. / Menna, M. / Fiorentino, F. / Ren, R. / Yu, D. / Hajian, T. / Vedadi, M. / Mazzoccanti, G. / Ciogli, A. / Weinhold, E. / Huben, M. / Blumenthal, R.M. / Zhang, X. / Mai, A. / Rotili, D. / Cheng, X.
History
DepositionMay 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Site-specific DNA-methyltransferase (adenine-specific)
B: Site-specific DNA-methyltransferase (adenine-specific)
C: Site-specific DNA-methyltransferase (adenine-specific)
E: DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')
D: DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')
F: DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')
G: DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')
H: DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')
I: DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,84927
Polymers231,9239
Non-polymers1,92618
Water14,592810
1
A: Site-specific DNA-methyltransferase (adenine-specific)
E: DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')
D: DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8337
Polymers77,3083
Non-polymers5264
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Site-specific DNA-methyltransferase (adenine-specific)
F: DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')
G: DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,24514
Polymers77,3083
Non-polymers93711
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Site-specific DNA-methyltransferase (adenine-specific)
H: DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')
I: DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7716
Polymers77,3083
Non-polymers4643
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.440, 161.434, 229.712
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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Protein , 1 types, 3 molecules ABC

#1: Protein Site-specific DNA-methyltransferase (adenine-specific)


Mass: 68749.023 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria)
Gene: BN1095_20232, BN1096_690041, BN1097_700039, E5F26_07025, E5F27_14470, E5F28_16275, E5F29_09620, E5F30_09400, E5F31_14185, E5F32_03810, E5F33_08870, E5F36_00990, E5F37_03060, E5F38_04245, E5F39_ ...Gene: BN1095_20232, BN1096_690041, BN1097_700039, E5F26_07025, E5F27_14470, E5F28_16275, E5F29_09620, E5F30_09400, E5F31_14185, E5F32_03810, E5F33_08870, E5F36_00990, E5F37_03060, E5F38_04245, E5F39_00835, E5F40_02785, E5F41_17405, E5F42_11180, E5F43_12285, E5F44_14865, E5F45_19095
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A031WG99, site-specific DNA-methyltransferase (adenine-specific)

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DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)- ... , 2 types, 6 molecules EGIDFH

#2: DNA chain DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')


Mass: 4325.825 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: (DA)(DT)(DG)(DG)(DG)(DA)(DC)(DT)(DT)(DT)(DT)(DT)(DG)(DA)
Source: (synth.) Clostridioides difficile (bacteria)
#3: DNA chain DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3')


Mass: 4232.795 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Clostridioides difficile (bacteria)

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Non-polymers , 4 types, 828 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-Q8Y / N-(3-phenylpropyl)adenosine


Mass: 385.417 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H23N5O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 810 / 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: 3.26 Å3/Da / Density % sol: 62.22 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 21-24% PEG 3350, 0.1 M Tris-HCl pH 7-7.5, 0.28M Potassium Citrate
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→45.89 Å / Num. obs: 125490 / % possible obs: 99.5 % / Redundancy: 12.7 % / Biso Wilson estimate: 40.43 Å2 / CC1/2: 0.99 / Net I/σ(I): 12.4
Reflection shellResolution: 2.35→2.43 Å / Num. unique obs: 12141 / CC1/2: 0.356

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.35→45.89 Å / SU ML: 0.3145 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.6003
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2041 1999 1.6 %
Rwork0.1744 123293 -
obs0.1749 125292 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.99 Å2
Refinement stepCycle: LAST / Resolution: 2.35→45.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13424 1704 123 810 16061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002915724
X-RAY DIFFRACTIONf_angle_d0.560421537
X-RAY DIFFRACTIONf_chiral_restr0.04262359
X-RAY DIFFRACTIONf_plane_restr0.00322463
X-RAY DIFFRACTIONf_dihedral_angle_d16.97046021
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.410.36871330.31238098X-RAY DIFFRACTION91.94
2.41-2.480.3231400.27488719X-RAY DIFFRACTION99.19
2.48-2.550.30251410.26088742X-RAY DIFFRACTION99.48
2.55-2.630.26781410.25318609X-RAY DIFFRACTION98.2
2.63-2.720.29581410.23338783X-RAY DIFFRACTION99.78
2.72-2.830.25231430.21468816X-RAY DIFFRACTION99.98
2.83-2.960.23471430.19778801X-RAY DIFFRACTION99.96
2.96-3.120.24571440.19348870X-RAY DIFFRACTION100
3.12-3.310.19451420.18598812X-RAY DIFFRACTION99.89
3.31-3.570.191440.1548885X-RAY DIFFRACTION99.89
3.57-3.930.1931450.15128884X-RAY DIFFRACTION99.93
3.93-4.50.14921450.12938970X-RAY DIFFRACTION100
4.5-5.660.17461460.13588998X-RAY DIFFRACTION99.99
5.66-45.890.16011510.15759306X-RAY DIFFRACTION99.46
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)
12.04476332741-0.540458874397-1.601939000061.91181025152-0.235810607921.447947443550.260406921605-0.2585815301920.3231616353670.00990566124494-0.145293262252-0.269169047579-0.5005509969140.690234313331-0.1164060843480.325376744257-0.1092845218420.02415505109570.4324023318980.06065374022170.3234399242585.30378183041-2.58274245383-25.4931691651
20.9177139219780.1489605872330.03420706272591.84497714081-1.654727569492.92809471028-0.01251840983690.06610606025140.289979612892-0.205377807428-0.0913280656953-0.460178911186-0.281418905950.2559947422520.1322274522690.444415963979-0.0612109986870.1182766106730.2246867619360.04014238127440.4292068498178.33104048089-0.0759767507359-28.4351914119
31.91139196766-0.5637502287260.4511994100680.3229699071320.6171809365334.95835887603-0.1742202627440.09668631452460.0948301380474-0.316300416274-0.112598120499-1.21193856727-0.3741823239520.6082062536840.225798901690.52961007615-0.02451513475570.212532464660.4200247632620.1938699590870.93440861519531.666231328632.8769669447-41.498885119
42.93846865777-2.05089324755-1.154020418863.225505247360.9784357730015.69008321901-0.0133783715383-0.6209755236360.698443560920.0235727451207-0.390326384018-0.867242248119-0.7066427541861.064003754880.197187117450.472021643442-0.1217174074-0.07236974576780.4223294787620.06932478087850.73881706541934.821949963636.7519094654-41.1622683119
51.36729329350.06678517142160.1854303034983.8050103833.076559690836.50304804430.003030213363830.05034347329010.05780511620380.194285629218-0.1369374918190.18297585386-0.535696190701-0.4064480482570.1528054878650.4905637625160.08335012598960.05882838721350.343065071664-0.03424365518680.336145472417-34.04342952265.0547630688834.2463575431
61.17147852555-0.633655229745-0.2516805694553.190902545181.175106763253.134641969130.05066255680920.004602965618880.19544760541-0.131377989950.016176262788-0.160506635922-0.4978597242980.025885700943-0.0950028403850.389936797476-0.01802122535220.06944026750090.289174774087-0.04775538969590.268423878328-22.6880502354-3.1655768445618.7883587099
70.240116440072-0.469598135342-0.5094072883961.500533755240.6615241925243.4211095785-0.116395387065-0.07288691689280.03470473052670.411527464310.0877180093414-0.0270678580610.08982455211120.05278223285550.0361864682390.324927546324-0.06033324203330.03796922532060.341234158956-0.01301236622270.314417648521-17.8623553887-23.840773137818.7271234864
82.87164243129-0.9959975305731.258450345783.841374485590.02213368975391.189430045010.07099227297680.647888205173-0.0676181298592-0.9940319058690.1032958303290.3275352336170.0186340442619-0.139203619489-0.1830372785820.417168632757-0.0303538809812-0.002946497073740.552329720057-0.03360025446750.264283007551-27.6620712795-27.2760265996-16.5942628743
91.2671114111-0.1967712806580.4724361787222.37236800298-1.278366936843.03768694478-0.008061839920570.0300390857528-0.112339107932-0.150874492099-0.0758026065993-0.1327338415980.1849591622940.2507892423810.07066365452620.191962921386-0.01271611879440.06990711231830.311235046246-0.0310836024460.226335118038-14.4283765768-35.5200226763.56882429401
102.83430761726-0.9078966756062.831440254321.10571724234-1.433400476855.63503279206-0.0005262430425240.1513294751740.2229319959220.0255485218735-0.128053748914-0.0679613054294-0.507532686211-0.001453187405350.1387359713330.5125668538630.08162061314930.06102696276130.3045483948410.1029253802260.3518169564-14.294801865313.9745216063-57.2552816556
111.78628570677-0.6918648693210.7938115169312.04846109994-0.8991207480832.45202455350.09329315224910.02432971343030.0806647905064-0.03406369984810.02667080709350.175686658074-0.215396532202-0.279415987584-0.117514698910.3667355092290.06491130527210.0558947742380.3019007930580.08240972792230.27329656273-13.02107924872.25026194247-41.7106648479
124.69767086398-1.159389282921.080896433932.45515532520.1009445003754.106447980010.116882416640.6016480946990.223053755581-0.520870079116-0.147897119376-0.4345131198570.1590658564340.6811540339760.02412526723140.5116935163540.1622807709380.04885784927270.4367983421350.07136014376560.3264463930.370511043304-9.0411619737-53.9337136734
131.59485117184-0.850794605067-0.03974692649712.19673440707-0.06495899121441.791343359060.0944295213529-0.02177691491730.0180397245201-0.02402514205820.00484753939533-0.07624239096440.07266085543170.134932387333-0.1023579733760.249052514556-0.0178290544768-0.0002785142849510.2281589159440.06700078397710.2256843228918.66516280871-18.5094506117-21.6987220664
141.988855840350.2635122644361.344812932933.181472214841.545687597056.63294777877-0.316830079565-0.6283198672740.1490037327491.43300154010.2170416504910.005209806333380.314003319556-0.3337456447410.08950967561851.112041998920.09669493466670.03798775313390.511407027692-0.04743973815670.52930638856921.356073743251.6066764889-14.0364721965
151.65368165387-0.185765522935-0.4906685196442.536612471991.75090693663.44419207847-0.208109557294-0.636556185142-0.01539083675111.071941191290.05234611918160.0530175199560.1371449883090.06187570891940.1703322438751.071350573410.0983463379450.09536802979640.5377746638290.03400418232290.5369146124421.139642860742.5679790947-14.9398620789
161.88916786139-1.339193489591.955730980765.035425849050.3028276309682.967187925920.0429198515803-0.2581178390860.2586081634040.450989381322-0.1120490772020.532167864437-0.419135438611-0.3152161556030.01753257979850.6527637104230.07208350416310.1387978791430.359389463777-0.01621605722890.51528986382116.920137420752.8309964631-30.8547903939
173.69391422892-2.296692703960.1452665188842.7370444093-0.05040241123531.315466294270.07611241887910.1072476568890.102456443789-0.22253143096-0.144402276070.116533354393-0.005626158400580.0493959595010.05539049350640.4722652473940.003574434768720.0810851647950.2790180795660.04016341054640.49429482820524.362363790730.5675485069-52.9872310406
187.695207019930.804781474109-1.885405910741.51451721186-3.27840259797.35978812003-0.1044728919170.053755695644-0.804345586764-0.0344466605352-0.03660333640190.2184702023921.040187376090.7829093838490.2143655038430.6584721949120.166530628630.04562606248980.3390573805990.099300487750.6031260088943.029842400513.1314964622-46.9375817448
192.57192563006-1.471928578470.9429952805292.3550434271-0.647995062772.046555770130.05812262184980.164403553619-0.13541730868-0.445893189589-0.1165015229630.339710258751-0.113984185392-0.08080786304690.0699472896640.5263983077750.0132947839020.03761744688210.2878120997820.02892789269840.5221070635517.810253917734.1706817-57.3354997966
201.50948533971-0.7140601049470.3011519386532.87962704158-0.7099275025313.431191323870.0483061218319-0.6266036523280.2312834896490.363932314812-0.05623299905721.231448508130.079115677081-0.858875795454-0.1657248162850.325598834023-0.04342435830310.190862042280.615232452936-0.05007493819230.508628092496-32.5627861085-20.35757873764.31862574774
210.436909969387-0.674206423210.8887974808743.63933900033-0.6278039438092.19918030145-0.1389479694490.0472238286194-0.3464866679220.0206934276701-0.03247799859060.6932426098210.188161345195-0.7939779586570.1364022183780.314626893935-0.122652279344-0.001956836926650.497059128572-0.08374137933450.38311863014-28.5748386356-19.23112942112.18162631596
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'F' and (resid 1 through 14 )FF1 - 14
22chain 'G' and (resid 1 through 14 )GG1 - 14
33chain 'H' and (resid 1 through 14 )HH1 - 14
44chain 'I' and (resid 1 through 14 )II1 - 14
55chain 'A' and (resid 28 through 130 )AA28 - 1301 - 103
66chain 'A' and (resid 131 through 273 )AA131 - 273104 - 242
77chain 'A' and (resid 274 through 359 )AA274 - 359243 - 328
88chain 'A' and (resid 360 through 428 )AA360 - 428329 - 397
99chain 'A' and (resid 429 through 577 )AA429 - 577398 - 546
1010chain 'B' and (resid 28 through 129 )BB28 - 1291 - 102
1111chain 'B' and (resid 130 through 273 )BB130 - 273103 - 246
1212chain 'B' and (resid 274 through 311 )BB274 - 311247 - 284
1313chain 'B' and (resid 312 through 577 )BB312 - 577285 - 550
1414chain 'C' and (resid 28 through 66 )CC28 - 661 - 39
1515chain 'C' and (resid 67 through 246 )CC67 - 24640 - 209
1616chain 'C' and (resid 247 through 311 )CC247 - 311210 - 274
1717chain 'C' and (resid 312 through 399 )CC312 - 399275 - 362
1818chain 'C' and (resid 400 through 428 )CC400 - 428363 - 391
1919chain 'C' and (resid 429 through 577 )CC429 - 577392 - 540
2020chain 'E' and (resid 1 through 14 )ED1 - 14
2121chain 'D' and (resid 1 through 14 )DE1 - 14

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