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

ID or keywords:

Entry

Database: PDB / ID: 8xtg

Title

Crystal structure of methyltransferase MpaG' in complex with SAH and DMMPA

Components

O-methyltransferase mpaG'

Keywords

BIOSYNTHETIC 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

Biological species

Penicillium brevicompactum (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

You, C. / Pan, Y.J. / Li, S.Y. / Feng, Y.G.

Funding support

China, 1items

Citation

Journal: 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

Deposition	Jan 10, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 28, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8xtg.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb8xtg.ent.gz		Display	PDB format
PDBx/mmJSON format	8xtg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8xtg_validation.pdf.gz	3.6 MB	Display	wwPDB validaton report
Full document	8xtg_full_validation.pdf.gz	3.6 MB	Display
Data in XML	8xtg_validation.xml.gz	99.4 KB	Display
Data in CIF	8xtg_validation.cif.gz	143.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xt/8xtg ftp://data.pdbj.org/pub/pdb/validation_reports/xt/8xtg	HTTPS FTP

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Related structure data

Related structure data	8xteC 8xtfC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: O-methyltransferase mpaG'

B: O-methyltransferase mpaG'

C: O-methyltransferase mpaG'

D: O-methyltransferase mpaG'

E: O-methyltransferase mpaG'

F: O-methyltransferase mpaG'

hetero molecules

266 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: O-methyltransferase mpaG'

B: O-methyltransferase mpaG'

hetero molecules

defined by author&software
Evidence: gel filtration
88.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: O-methyltransferase mpaG'

D: O-methyltransferase mpaG'

hetero molecules

defined by author&software
88.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: O-methyltransferase mpaG'

F: O-methyltransferase mpaG'

hetero molecules

defined by author&software
88.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	199.541, 199.541, 67.154
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	145
Space group name H-M	P3₂
Space group name Hall	P3₂

#1: Protein	O-methyltransferase mpaG' / Mycophenolic acid biosynthesis cluster protein G' Mass: 43693.082 Da / Num. of mol.: 6 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.: 6 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-A1LWD / O-desmethyl mycophenolic acid / (~{E})-4-methyl-6-[7-methyl-4,6-bis(oxidanyl)-3-oxidanylidene-1~{H}-2-benzofuran-5-yl]hex-4-enoic acid Mass: 306.311 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₆H₁₈O₆ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1776 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.94 Å³/Da / Density % sol: 58.22 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion Details: 15% PEG3350 (w/v), 0.1 M sodium cacodylate, pH 6.0 and 0.2 M magnesium chloride

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97853 Å / Relative weight: 1
Reflection	Resolution: 2→47.97 Å / Num. obs: 202861 / % possible obs: 99.9 % / Redundancy: 5.2 % / B_iso Wilson estimate: 23.29 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.131 / R_pim(I) all: 0.064 / R_rim(I) all: 0.146 / Χ²: 0.97 / Net I/σ(I): 10.8
Reflection shell	Resolution: 2→2.03 Å / % possible obs: 98.2 % / Redundancy: 4.9 % / R_merge(I) obs: 0.942 / Num. measured all: 48859 / Num. unique obs: 9929 / CC_1/2: 0.666 / R_pim(I) all: 0.472 / R_rim(I) all: 1.056 / Χ²: 0.9 / Net I/σ(I) obs: 1.8

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
Aimless		data scaling
autoPROC		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2→47.93 Å / Cross valid method: FREE R-VALUE / σ(F): 164.13 / Phase error: 35.2064
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2112	10417	5.14 %	RANDOM
R_work	0.1618	192412	-	-
obs	0.1649	202829	99.88 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 30.46 Å²

Refinement step

Cycle: LAST / Resolution: 2→47.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18239	0	288	1776	20303

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0034	18983
X-RAY DIFFRACTION	f_angle_d	0.6516	25822
X-RAY DIFFRACTION	f_chiral_restr	0.0432	2814
X-RAY DIFFRACTION	f_plane_restr	0.0056	3391
X-RAY DIFFRACTION	f_dihedral_angle_d	5.5379	2748

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2-2.03	0.2625	528	0.232	9487	X-RAY DIFFRACTION	93.09
2.03-2.07	0.2553	498	0.2212	9643	X-RAY DIFFRACTION	95.06
2.07-2.11	0.2826	474	0.2145	9708	X-RAY DIFFRACTION	95.34
2.11-2.15	0.2689	541	0.2094	9604	X-RAY DIFFRACTION	94.64
2.15-2.2	0.2568	526	0.2025	9570	X-RAY DIFFRACTION	94.72
2.2-2.25	0.2505	528	0.1934	9665	X-RAY DIFFRACTION	94.81
2.25-2.31	0.2554	466	0.1896	9684	X-RAY DIFFRACTION	95.4
2.31-2.37	0.2565	558	0.1849	9565	X-RAY DIFFRACTION	94.45
2.37-2.44	0.2547	541	0.183	9566	X-RAY DIFFRACTION	94.62
2.44-2.52	0.2222	499	0.176	9697	X-RAY DIFFRACTION	95.11
2.52-2.61	0.216	490	0.1741	9646	X-RAY DIFFRACTION	95.16
2.61-2.71	0.2391	507	0.1696	9628	X-RAY DIFFRACTION	95
2.71-2.83	0.2119	510	0.1657	9703	X-RAY DIFFRACTION	95.01
2.83-2.98	0.2087	548	0.1589	9557	X-RAY DIFFRACTION	94.58
2.98-3.17	0.2008	549	0.1526	9642	X-RAY DIFFRACTION	94.58
3.17-3.41	0.2036	530	0.1401	9594	X-RAY DIFFRACTION	94.76
3.41-3.76	0.185	567	0.1342	9599	X-RAY DIFFRACTION	94.36
3.76-4.3	0.1552	502	0.1214	9634	X-RAY DIFFRACTION	95.03
4.3-5.42	0.1817	577	0.1295	9552	X-RAY DIFFRACTION	94.21
5.42-47.93	0.2165	471	0.1803	9675	X-RAY DIFFRACTION	95.21

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.288258787238	-0.00724575677666	-0.222419802625	0.852579829682	-0.121641925942	0.941823721971	-0.0189620015621	0.0295472623363	-0.0774924493215	0.0166646524822	-0.00221231105965	0.0724369842017	0.164117367072	-0.215700666501	0.0115641494086	0.304843348938	-0.0663035096539	-0.0203799224291	0.303121337447	-0.0113896817062	0.0875341038944	35.5061456245	-0.602474302496	1.56188559581
2	0.667520384478	0.537677471667	0.363111433986	1.39451914142	0.743516650296	0.970902443603	0.000728627666633	-0.00270741209781	-0.0398363958646	0.0031475095074	-0.0232929173315	-0.0308438811219	0.0501451787083	-0.0382314017887	0.0226110479881	0.235932276291	-0.0361240806696	-0.00286573651881	0.244768924153	0.00614681102889	0.0849687428797	39.7065845644	-16.5742362463	-20.6539951049
3	2.94601593193	-1.69575603196	-1.28166129774	5.65532833345	3.50010859533	3.20739344268	-0.450502918813	-0.281794016797	-0.194110850463	0.503827994601	0.08626756019	0.56438382552	0.105638903565	-0.516686838819	0.328553797915	0.310218943495	0.028545744296	0.0207026980786	0.637080539706	-0.0156131134748	0.200871181854	15.3137519833	4.75363041467	4.31681799453
4	0.154575103656	-0.0361026799849	-0.0820405775034	0.251452611095	0.209867015252	0.504988407372	0.0294738648876	0.0464956143199	0.00473742507133	-0.0764453552441	-0.0281634019138	0.0200635413986	-0.0217441092754	-0.0997796863844	0.00105543998748	0.232662539674	-0.0205067056106	-0.0120110009202	0.275949454344	0.0163982607902	0.0860970961411	36.0087260099	18.6009116833	0.27490507037
5	5.36321313567	-1.95904732523	-0.91530446961	1.0617918977	0.609545733607	0.404973216658	0.398206762688	0.386572101958	0.601660248409	-0.368869549772	-0.0870881516694	-0.258500169782	-0.275979693298	-0.0900643962632	-0.175266770065	0.26019321758	-0.0191470600992	0.00121692591479	0.356069301584	0.0679325046838	0.133229729422	34.4336115056	39.8197171355	11.2591357344
6	0.344972344215	-0.12976080845	-0.479740287728	0.882210031989	0.413266165122	1.11575658305	-0.0327720279078	-0.0314777347719	0.0662410251071	0.0904532312851	0.0214975790556	0.0877793995049	0.135739968262	0.0608802321584	-0.000876299229508	0.262386520023	-0.0041241901293	-0.0240472624695	0.336048313593	0.0122476125351	0.0603327968041	33.0337095156	22.3276729356	23.0937032805
7	0.747557157755	-0.0575818814166	0.250109286753	0.352233834754	0.0284227202166	0.609894593854	-0.00388064940121	0.025824453319	0.0603794418408	0.00473164272321	-0.0152501872525	-0.0251226540313	-0.0670365431928	0.0980219913573	0.0177688627838	0.240039091878	-0.0197148519205	0.00117182058394	0.284412720795	0.0126132372326	0.0869631605637	71.2904947069	33.6226795528	-4.30764225012
8	0.894014939352	-0.421409775848	0.20784879065	1.64049847873	-0.306192687933	0.638958035553	-0.01000604015	0.0740466003856	0.00986430582443	-0.0841844963924	0.00831518156086	0.0669748463986	-0.146420656585	0.0804650187184	0.000199376703456	0.258302027482	-0.0459572111307	0.00241376377548	0.242210802296	0.0107201094769	0.0799800350129	59.9518314149	44.5050427287	-26.9246979351
9	7.01765994884	-2.56759715546	3.56207329533	4.7602969455	-1.99828984879	2.15740826385	-0.626503263695	-0.553680414645	0.646368895533	0.432903508465	0.17681176902	-0.577819612103	-0.522015462795	0.434800915079	0.394134590866	0.405724117474	-0.0894690383176	-0.0794545951141	0.536599369274	0.0260265388973	0.242263475975	92.0434639085	43.6521791252	-0.684411200131
10	0.493085766	-0.113860125444	0.195414528284	0.282082097019	-0.125561101692	0.182335354281	0.0188048105219	0.130730791315	-0.0588850311514	-0.0449036396807	-0.0231252038851	-0.00181852653987	0.0368445153917	0.121108214222	0.0148695760919	0.225973250995	-0.0042640273604	0.00469763225035	0.349156447625	-0.0214443070927	0.0853964812209	85.8169686879	19.4438693418	-4.57437395165
11	5.47944173987	2.27436577837	-0.121402239289	1.25157633013	0.338063341861	0.499361821087	-0.138698685549	0.767371867574	-0.762126430008	-0.150530273191	0.166651513715	-0.173737182889	-0.00594721700657	0.217459870328	0.0071454009224	0.245011456538	0.0468491826196	-0.0391186268522	0.381382642196	-0.0621214715976	0.179113695072	101.359715425	4.8262747966	6.50617280406
12	0.708696931005	-0.313115575344	0.281067322701	0.640235279139	-0.555076336588	0.918767193861	0.0501953033978	-0.0195518723278	-0.0212095226165	0.0938827523775	-0.0646772569971	0.00253652276522	-0.107830560969	-0.00867464345079	0.0165435273696	0.244469227005	-0.00657941878392	0.00462439477918	0.336710594477	-0.0187111347327	0.0936040057043	90.5578000622	18.5693123746	18.4493868038
13	7.10710596276	3.43257921013	-3.39799414463	5.84344931577	-1.92839052278	2.81061539998	-0.307128106112	-1.12405242014	-0.752747827934	0.221955373777	-0.246453218835	-0.603626186725	0.087807173309	0.00517954249189	0.514118556345	0.631378669542	0.172136154268	-0.0559092832075	0.569973388201	0.0268991202979	0.337812965242	88.9966565333	-45.0661076588	1.45099584341
14	5.97079029185	1.23281839618	-0.154693944794	0.310886631352	-0.0112681167348	0.0222232383634	-0.0883478089439	0.169543270257	-0.204834790671	0.105222005802	0.0611643736155	-0.00813114690805	-0.0917372064937	0.175577153627	0.0177107756075	0.579133912866	0.00958434474292	0.00917951891581	0.437200567989	-0.00496624094284	0.199778739003	83.8306890554	-24.1434661765	-8.89567431806
15	2.30598377312	0.648469756442	-0.235967807474	0.459473474164	-0.885929661675	2.70040169259	-0.235021903333	0.309093308535	-0.0423041923873	-0.141811854322	0.298091153114	-0.025556970848	-0.202714366905	-0.622495074072	-0.0507192768844	0.47669248032	-0.0980783359424	0.0279293377505	0.663054694073	-0.0265594782867	0.228890577529	72.8720191262	-30.7488743799	-22.4101043736
16	1.43145853604	0.693036187702	1.08683375515	2.00052758652	0.0411112554712	0.982346413708	0.0769258560192	0.212187520705	-0.0612720797582	-0.402602764797	-0.0706928860436	-0.0937459437745	-0.0884411054788	-0.186036039771	-0.0200750794251	0.456023804412	0.0192988421672	0.0397063319545	0.478363744193	0.0221533450817	0.166646688851	72.4951256056	-32.6434612523	-12.2256005219
17	2.90983220558	1.93702978955	2.01727406767	2.14624709907	1.29453590904	1.49353373882	-0.064318589477	-0.841418380152	0.424488907896	0.132022801149	-0.176244867084	0.346207620963	-0.0401942539722	-0.102583306709	0.209902524612	0.463152895776	0.0087331054501	0.0699169486093	0.505715331062	-0.0606804939966	0.290773025593	74.6704079968	-12.4772837853	9.06865298103
18	0.536323615756	0.0748491787596	-0.201703691692	2.12385866046	-2.22761627532	2.3381019902	-0.0200148990867	0.0301080355225	-0.0959646415951	-0.152506615076	0.0270594538133	0.0173576612747	0.302725992141	0.137580335682	0.0229850826439	0.497432343429	0.00571633510515	-0.0289795669535	0.456641740523	-0.0374128586378	0.186598047522	64.4119116875	-32.9179860071	7.02576236944
19	1.67311632912	-0.0257946166964	-0.814784671577	7.73083819619	-1.26790368508	0.697889803386	0.051776547325	0.34315225072	-0.00274454629272	-0.0457662468264	0.0468950483336	0.379629158618	-0.050938649909	-0.0798027780133	-0.104978111309	0.37189871422	-0.0188006339226	-0.0390224495896	0.434755192784	0.015388036115	0.173287637681	53.0569473767	-40.2530916243	11.9566684547
20	2.05499018717	-0.154143494953	-1.43357580331	0.987246957631	0.29718391665	1.02459617688	-0.0111166627232	-0.3253044214	0.0195201226802	0.108581239843	0.0575888754677	0.077080398385	-0.0252672065679	0.188933971005	-0.0408376456268	0.42319131898	0.0489872201025	0.0257667840895	0.452817815298	0.0202637606737	0.172700894237	63.5218360976	-33.190084559	21.8184816804
21	1.91396353744	1.24444322497	-0.750125998481	3.16460352231	-2.07063941499	1.38631612069	-0.0727391503784	-0.308107138068	0.0512311695743	-0.0314947592008	-0.19628415924	-0.0791771147705	0.228509163714	0.386541155829	0.258603915251	0.44674197859	0.0171759707246	0.00158172500711	0.516705373215	0.0181712308129	0.184171267054	72.6185224016	-33.2465930034	19.5950007458
22	1.57489912673	0.336749413988	-0.0286616121952	1.72319378974	0.00630999542395	1.59835652492	0.0265162714773	-0.0726220078739	-0.0227303474266	-0.0277536299902	-0.0154356180223	-0.130362395835	0.0521103032125	0.407589323625	-0.015929578951	0.414202318176	0.0372394931663	0.0296174955936	0.543368851821	-0.0114532878299	0.162606248151	88.9008816208	-23.7111364775	-0.956287684867
23	3.40230148306	-0.145309927081	-1.49776354174	0.711976164417	-0.231571746201	0.989126655998	0.072396462248	0.0734517798384	0.110051987098	0.0026680934911	-0.0184159561758	0.00565352779025	-0.0165584479859	-0.129149456756	-0.0444028797854	0.386494144053	-0.00878427254484	0.00636723889152	0.403301700384	-0.0193157250344	0.169572576036	102.581405689	-14.9649574734	-23.4496997339

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 5 through 181 )	A	A	5 - 181	1 - 177
2	2	chain 'A' and (resid 182 through 398 )	A	A	182 - 398	178 - 394
3	3	chain 'B' and (resid 4 through 42 )	B	D	4 - 42	1 - 39
4	4	chain 'B' and (resid 43 through 252 )	B	D	43 - 252	40 - 249
5	5	chain 'B' and (resid 253 through 284 )	B	D	253 - 284	250 - 281
6	6	chain 'B' and (resid 285 through 398 )	B	D	285 - 398	282 - 395
7	7	chain 'C' and (resid 6 through 201 )	C	G	6 - 201	1 - 196
8	8	chain 'C' and (resid 202 through 398 )	C	G	202 - 398	197 - 393
9	9	chain 'D' and (resid 4 through 42 )	D	J	4 - 42	1 - 39
10	10	chain 'D' and (resid 43 through 252 )	D	J	43 - 252	40 - 249
11	11	chain 'D' and (resid 253 through 284 )	D	J	253 - 284	250 - 281
12	12	chain 'D' and (resid 285 through 398 )	D	J	285 - 398	282 - 395
13	13	chain 'E' and (resid 8 through 42 )	E	M	8 - 42	1 - 35
14	14	chain 'E' and (resid 43 through 69 )	E	M	43 - 69	36 - 62
15	15	chain 'E' and (resid 70 through 108 )	E	M	70 - 108	63 - 101
16	16	chain 'E' and (resid 109 through 142 )	E	M	109 - 142	102 - 135
17	17	chain 'E' and (resid 143 through 181 )	E	M	143 - 181	136 - 174
18	18	chain 'E' and (resid 182 through 221 )	E	M	182 - 221	175 - 214
19	19	chain 'E' and (resid 222 through 284 )	E	M	222 - 284	215 - 277
20	20	chain 'E' and (resid 285 through 344 )	E	M	285 - 344	278 - 337
21	21	chain 'E' and (resid 345 through 398 )	E	M	345 - 398	338 - 391
22	22	chain 'F' and (resid 5 through 181 )	F	P	5 - 181	1 - 177
23	23	chain 'F' and (resid 182 through 398 )	F	P	182 - 398	178 - 389

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