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- PDB-7agp: Structure of the AcylTransferase domain of Mycocerosic Acid Synth... -

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Basic information

Entry
Database: PDB / ID: 7agp
TitleStructure of the AcylTransferase domain of Mycocerosic Acid Synthase from Mycobacterium tuberculosis
ComponentsMycocerosic acid synthase
KeywordsTRANSFERASE / Mycocerosic Acid Synthase / AcylTransferase domain / polyketide synthase / Mycobacterium tuberculosis
Function / homology
Function and homology information


mycocerosate synthase activity / mycocerosate synthase / DIM/DIP cell wall layer assembly / fatty acid synthase activity / ligase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity / hydrolase activity ...mycocerosate synthase activity / mycocerosate synthase / DIM/DIP cell wall layer assembly / fatty acid synthase activity / ligase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity / hydrolase activity / plasma membrane / cytoplasm
Similarity search - Function
: / Malonyl-CoA ACP transacylase, ACP-binding / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / : ...: / Malonyl-CoA ACP transacylase, ACP-binding / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / GroES-like superfamily / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Mycocerosic acid synthase
Similarity search - Component
Biological speciesMycobacterium bovis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBrison, Y. / Nahoum, V. / Mourey, L. / Maveyraud, L.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-09-BLAN-0298-01 France
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Molecular Basis for Extender Unit Specificity of Mycobacterial Polyketide Synthases.
Authors: Grabowska, A.D. / Brison, Y. / Maveyraud, L. / Gavalda, S. / Faille, A. / Nahoum, V. / Bon, C. / Guilhot, C. / Pedelacq, J.D. / Chalut, C. / Mourey, L.
History
DepositionSep 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mycocerosic acid synthase
B: Mycocerosic acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0654
Polymers92,9412
Non-polymers1242
Water4,288238
1
A: Mycocerosic acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5322
Polymers46,4701
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mycocerosic acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5322
Polymers46,4701
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.028, 157.14, 114.255
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Mycocerosic acid synthase


Mass: 46470.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97) (bacteria)
Strain: ATCC BAA-935 / AF2122/97 / Gene: mas, BQ2027_MB2965C / Production host: Escherichia coli (E. coli) / References: UniProt: Q02251, mycocerosate synthase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.53 Å3/Da / Density % sol: 65.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 1.1 M sodium succinate 0.1 M sodium acetate buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.4→49.3 Å / Num. obs: 51153 / % possible obs: 99.1 % / Redundancy: 3.54 % / Biso Wilson estimate: 74.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rrim(I) all: 0.05 / Rsym value: 0.042 / Net I/σ(I): 15.77
Reflection shellResolution: 2.4→2.54 Å / Redundancy: 3.48 % / Rmerge(I) obs: 0.845 / Mean I/σ(I) obs: 1.43 / Num. unique obs: 8121 / CC1/2: 0.658 / Rrim(I) all: 0.998 / Rsym value: 0.845 / % possible all: 98.4

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
REFMAC5.8.0258refinement
PHASERphasing
XDSJan 31, 2020data scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TZW

3tzw


Resolution: 2.4→49.3 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.944 / SU R Cruickshank DPI: 0.243 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.243 / SU Rfree Blow DPI: 0.187 / SU Rfree Cruickshank DPI: 0.189
RfactorNum. reflection% reflectionSelection details
Rfree0.2193 2534 -RANDOM
Rwork0.1966 ---
obs0.1976 51153 99.1 %-
Displacement parametersBiso mean: 85.1 Å2
Baniso -1Baniso -2Baniso -3
1--14.1241 Å20 Å20 Å2
2--6.9346 Å20 Å2
3---7.1895 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.4→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6291 0 8 238 6537
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0116478HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.068864HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2132SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1123HARMONIC5
X-RAY DIFFRACTIONt_it6478HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion873SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5163SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.19
X-RAY DIFFRACTIONt_other_torsion16.89
LS refinement shellResolution: 2.4→2.42 Å
RfactorNum. reflection% reflection
Rfree0.3815 50 -
Rwork0.3748 --
obs0.3751 1024 93.05 %
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)
12.0787-1.48420.13382.3515-1.23371.31030.02360.14860.0260.1486-0.0444-0.08160.026-0.08160.02080.05940.0226-0.06310.02970.0290.043830.3616-29.2197-6.7949
21.5901-0.5343-0.2142.32710.1231.6034-0.00740.5384-0.10070.5384-0.1837-0.1718-0.1007-0.17180.19110.1698-0.0151-0.0417-0.1184-0.0318-0.1167-29.42316.458412.4533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|444 - A|872 }A444 - 872
2X-RAY DIFFRACTION2{ B|444 - B|872 }B444 - 872

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