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- PDB-7s6b: Crystal structure of modular polyketide synthase apo-Lsd14 from t... -

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Basic information

Entry
Database: PDB / ID: 7s6b
TitleCrystal structure of modular polyketide synthase apo-Lsd14 from the Lasalocid biosynthesis pathway, trapped in the transacylation step
Components(Polyketide synthase) x 3
KeywordsBIOSYNTHETIC PROTEIN / Modular polyketide synthase / ketosynthase / acyltransferase / acyl carrier protein
Function / homology
Function and homology information


macrolide biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / Polyketide synthase, docking domain superfmaily / Polyketide synthase, docking domain / Erythronolide synthase docking domain / PKS_PP_betabranch / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension ...Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / Polyketide synthase, docking domain superfmaily / Polyketide synthase, docking domain / Erythronolide synthase docking domain / PKS_PP_betabranch / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Phosphopantetheine attachment site / Thiolase-like / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Putative polyketide synthase
Similarity search - Component
Biological speciesStreptomyces lasalocidi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsBagde, S.R. / Mathews, I.I. / Kim, C.-Y.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM138990 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Science / Year: 2021
Title: Modular polyketide synthase contains two reaction chambers that operate asynchronously.
Authors: Saket R Bagde / Irimpan I Mathews / J Christopher Fromme / Chu-Young Kim /
Abstract: Type I modular polyketide synthases are homodimeric multidomain assembly line enzymes that synthesize a variety of polyketide natural products by performing polyketide chain extension and β-keto ...Type I modular polyketide synthases are homodimeric multidomain assembly line enzymes that synthesize a variety of polyketide natural products by performing polyketide chain extension and β-keto group modification reactions. We determined the 2.4-angstrom-resolution x-ray crystal structure and the 3.1-angstrom-resolution cryo–electron microscopy structure of the Lsd14 polyketide synthase, stalled at the transacylation and condensation steps, respectively. These structures revealed how the constituent domains are positioned relative to each other, how they rearrange depending on the step in the reaction cycle, and the specific interactions formed between the domains. Like the evolutionarily related mammalian fatty acid synthase, Lsd14 contains two reaction chambers, but only one chamber in Lsd14 has the full complement of catalytic domains, indicating that only one chamber produces the polyketide product at any given time.
History
DepositionSep 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyketide synthase
B: Polyketide synthase
C: Polyketide synthase
D: Polyketide synthase
E: Polyketide synthase


Theoretical massNumber of molelcules
Total (without water)332,2375
Polymers332,2375
Non-polymers00
Water14,934829
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.74, 92.85, 107.45
Angle α, β, γ (deg.)99.63, 94.93, 106.07
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Polyketide synthase /


Mass: 100184.992 Da / Num. of mol.: 2 / Fragment: KS and AT domains, residues 1-924
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lasalocidi (bacteria) / Gene: lsd14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B6ZK67
#2: Protein Polyketide synthase /


Mass: 56170.590 Da / Num. of mol.: 2 / Fragment: KR domain, residues 925-1468
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lasalocidi (bacteria) / Gene: lsd14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B6ZK67
#3: Protein Polyketide synthase /


Mass: 19525.816 Da / Num. of mol.: 1 / Fragment: ACP domain, residues 1469-1647
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lasalocidi (bacteria) / Gene: lsd14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B6ZK67
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 829 / Source method: isolated from a natural source / Formula: H2O
Compound detailsThe authors state that there are two copies of the multidomain modular polyketide synthase Lsd14 in ...The authors state that there are two copies of the multidomain modular polyketide synthase Lsd14 in the unit cell, forming a dimer. The Lsd14 polypeptide chain is 1667 residues in length and includes the ketosynthase (KS), acyltransferase (AT), ketoreductase (KR), acyl carrier protein (ACP) domains, and the linkers connecting these domains. We modelled two copies each of KS, AT and KR and one copy of the ACP. We were not able to model the second ACP and parts of AT-to-KR and KR-to-ACP linkers due to lack of clear electron density map. Hence we were not able to assign polypeptide chain identity for the entire sequence. We built the KS-AT di-domains, KR and the ACP with separate chain IDs.

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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: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.2 M lithium sulfate, 0.015 M magnesium sulfate, 0.1 M sodium acetate, pH 4.0, and 22% polyacrylic acid 5100

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
31001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.9795
SYNCHROTRONALS 5.0.221.005
SYNCHROTRONAPS 17-ID31
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELMay 2, 2018
DECTRIS PILATUS3 6M2PIXELMar 15, 2018
DECTRIS PILATUS 6M3PIXELFeb 17, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
21.0051
311
ReflectionResolution: 2.35→39.2 Å / Num. obs: 130003 / % possible obs: 98.1 % / Redundancy: 26.3 % / CC1/2: 0.999 / Net I/σ(I): 18.5
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 15.2 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 9300 / CC1/2: 0.683 / % possible all: 94.2

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
autoPROCdata reduction
XDSdata scaling
autoPROCdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.35→39.2 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.334 / SU Rfree Blow DPI: 0.227
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 6501 -RANDOM
Rwork0.2059 ---
obs0.2076 130003 98.1 %-
Displacement parametersBiso mean: 77.77 Å2
Baniso -1Baniso -2Baniso -3
1--13.2409 Å2-10.5903 Å2-0.0883 Å2
2--4.5691 Å2-2.6495 Å2
3---8.6718 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.35→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21194 0 0 829 22023
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00742311HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8976399HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d12473SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes7067HARMONIC5
X-RAY DIFFRACTIONt_it21681HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion2882SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact32513SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.77
X-RAY DIFFRACTIONt_other_torsion15.03
LS refinement shellResolution: 2.35→2.37 Å
RfactorNum. reflection% reflection
Rfree0.3559 131 -
Rwork0.3517 --
obs0.3519 2601 94.66 %
Refinement TLS params.

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)
10.56420.08160.08721.02680.11951.12540.02460.2106-0.10880.2106-0.0027-0.1039-0.1088-0.1039-0.02190.07270.08990.0341-0.07020.0175-0.09337.545613.8163-5.592
20.8561-1.02890.00512.1581-0.24080.95620.129-0.12850.0645-0.1285-0.26240.0290.06450.0290.13350.0180.04410.0318-0.11030.0349-0.103138.1704-26.0282-27.4272
31.2541-1.3337-0.04791.77940.01160.24760.0531-0.05510.1565-0.0551-0.1123-0.07850.1565-0.07850.05920.10760.05190.0184-0.0610.0298-0.102434.4286-30.6579-22.253
44.40052.5753-1.07262.0714-0.86661.095-0.06110.21680.16850.2168-0.17010.17460.16850.17460.23120.20640.089-0.0371-0.13490.0679-0.099622.42969.380225.929
50.9519-0.843-0.15671.7008-0.06491.8210.00760.17270.39990.1727-0.0528-0.11790.3999-0.11790.04520.2980.01770.0264-0.19510.0119-0.20935.9338-1.699121.0643
61.49120.42750.85173.3551.61214.4032-0.16970.4330.04890.4330.0238-0.22850.0489-0.22850.14590.30620.14040.0415-0.1525-0.03-0.2718-1.028619.601744.624
70.8361-0.03540.37993.3594-1.55952.5555-0.08320.0937-0.46410.0937-0.33460.1753-0.46410.17530.41780.25020.11830.0029-0.19940.083-0.2157.396651.871448.4085
82.806-1.2860.23463.8752-2.95435.6057-0.28540.4496-1.35880.44960.2635-0.6705-1.3588-0.67050.02190.52480.40810.025-0.36160.0904-0.3898-5.696865.124445.1217
9-0.39870.3641-0.55172.73541.2580.8143-0.0645-0.222-0.0736-0.2220.0198-0.2073-0.0736-0.20730.04470.32610.14550.02-0.0688-0.0116-0.2326-2.904133.010840.5998
1017.23281.00719.246911.51652.473612.78140.03511.1074-1.01591.10740.06091.3957-1.01591.3957-0.0959-0.34140.0698-0.0448-0.2549-0.02910.0222-36.62941.77441.2562
114.7987-6.00780.05428.8414-0.74680.92630.1029-0.17880.0138-0.1788-0.0305-0.1190.0138-0.119-0.0725-0.35370.0102-0.117-0.2695-0.1044-0.0526-16.6629-41.817-1.6319
125.325-2.8370.0115.1650.22973.4420.01060.1660.12610.166-0.14130.15010.12610.15010.1307-0.1280.1383-0.098-0.3066-0.11940.1081-7.5816-53.43144.0027
137.356-9.2187-3.014618.92676.31355.80010.4668-1.4216-0.4148-1.4216-0.2928-0.1318-0.4148-0.1318-0.174-0.16880.1952-0.1485-0.35050.0149-0.0778-17.7544-42.132-8.6322
147.2047-9.9387-7.506512.8383-7.951115.36370.02270.57340.07450.57340.1986-0.39610.0745-0.3961-0.22130.060.24030.5456-0.6618-0.1431-0.2532-34.6111-33.069319.4703
153.5813.1199-9.48485.22773.670110.79310.06121.0029-0.9261.00290.4392-0.2378-0.926-0.2378-0.50040.41670.0260.5589-0.1562-0.21010.0145-34.4581-35.551428.5966
164.9331-3.3927-4.79494.24510.35012.86420.03171.52270.21591.5227-0.10290.09140.21590.09140.07120.0538-0.00910.3625-0.4618-0.09130.0294-27.14-47.721219.778
175.3039-2.1722-1.6798.1495-0.68565.29110.17170.7529-0.50870.7529-0.151-0.2132-0.5087-0.2132-0.0207-0.16880.147-0.0001-0.4189-0.12560.0161-21.439-34.37415.6094
184.44941.7115-4.13761.7488-2.685.4189-0.1348-0.4150.4849-0.415-0.01270.07630.48490.07630.1476-0.04950.09870.0030.1486-0.1044-0.2261-18.55185.4255-31.4319
195.96980.27971.50332.3182-0.98382.4430.2165-0.25490.1115-0.2549-0.03320.28470.11150.2847-0.1833-0.11460.0711-0.0363-0.1471-0.0409-0.1971-28.195712.851-37.5515
202.86448.9676-5.447711.2689-1.10676.7643-0.2514-0.88470.1653-0.88470.2743-0.74830.1653-0.7483-0.02290.1180.1904-0.06290.0056-0.1116-0.110116.4512-22.1344-44.0013
2114.14255.5822-2.19411.6121-0.26111.24540.2997-1.2773-0.2344-1.27730.2941-0.5196-0.2344-0.5196-0.59380.73290.2106-0.0958-0.0782-0.1008-0.166820.0959-23.994-50.5902
222.73060.6849-3.13948.5852.484811.1949-0.0334-0.31230.316-0.3123-0.0774-0.45510.316-0.45510.11080.0660.13290.0148-0.0588-0.0895-0.174121.3761-29.2246-37.3343
230.89165.52547.56714.7129-3.810120.80450.0453-1.37130.2856-1.37130.0914-1.15590.2856-1.1559-0.13680.0991-0.0609-0.1733-0.1943-0.0918-0.309913.198-33.9053-42.233
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|14 - 463}A14 - 463
2X-RAY DIFFRACTION2{A|464 - 746}A464 - 746
3X-RAY DIFFRACTION3{A|747 - 913}A747 - 913
4X-RAY DIFFRACTION4{B|8 - 64}B8 - 64
5X-RAY DIFFRACTION5{B|65 - 473}B65 - 473
6X-RAY DIFFRACTION6{B|474 - 547}B474 - 547
7X-RAY DIFFRACTION7{B|548 - 701}B548 - 701
8X-RAY DIFFRACTION8{B|702 - 825}B702 - 825
9X-RAY DIFFRACTION9{B|826 - 913}B826 - 913
10X-RAY DIFFRACTION10{C|925 - 954}C925 - 954
11X-RAY DIFFRACTION11{C|955 - 1040}C955 - 1040
12X-RAY DIFFRACTION12{C|1041 - 1151}C1041 - 1151
13X-RAY DIFFRACTION13{C|1152 - 1195}C1152 - 1195
14X-RAY DIFFRACTION14{C|1196 - 1222}C1196 - 1222
15X-RAY DIFFRACTION15{C|1223 - 1264}C1223 - 1264
16X-RAY DIFFRACTION16{C|1265 - 1325}C1265 - 1325
17X-RAY DIFFRACTION17{C|1326 - 1454}C1326 - 1454
18X-RAY DIFFRACTION18{D|925 - 1067}D925 - 1067
19X-RAY DIFFRACTION19{D|1068 - 1456}D1068 - 1456
20X-RAY DIFFRACTION20{E|1482 - 1505}E1482 - 1505
21X-RAY DIFFRACTION21{E|1506 - 1520}E1506 - 1520
22X-RAY DIFFRACTION22{E|1521 - 1547}E1521 - 1547
23X-RAY DIFFRACTION23{E|1548 - 1567}E1548 - 1567

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