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- PDB-7bvh: Crystal structure of arabinosyltransferase EmbC2-AcpM2 complex fr... -

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Entry
Database: PDB / ID: 7bvh
TitleCrystal structure of arabinosyltransferase EmbC2-AcpM2 complex from Mycobacterium smegmatis complexed with di-arabinose
Components
  • Integral membrane indolylacetylinositol arabinosyltransferase EmbC
  • Meromycolate extension acyl carrier protein
KeywordsTRANSFERASE / cell wall synthesis / arabinosyltransferase / drug target
Function / homology
Function and homology information


indolylacetylinositol arabinosyltransferase / indolylacetylinositol arabinosyltransferase activity / arabinosyltransferase activity / Actinobacterium-type cell wall biogenesis / lipid A biosynthetic process / acyl binding / acyl carrier activity / Transferases; Glycosyltransferases; Pentosyltransferases / cell wall organization / metal ion binding ...indolylacetylinositol arabinosyltransferase / indolylacetylinositol arabinosyltransferase activity / arabinosyltransferase activity / Actinobacterium-type cell wall biogenesis / lipid A biosynthetic process / acyl binding / acyl carrier activity / Transferases; Glycosyltransferases; Pentosyltransferases / cell wall organization / metal ion binding / membrane / plasma membrane / cytosol
Similarity search - Function
arabinofuranosyltransferase like domain / Arabinofuranosyltransferase, central domain / Arabinofuranosyltransferase, domain 1 / Arabinosyltransferase, C-terminal / Arabinosyltransferas, concanavalin like domain / Arabinosyltransferase, C-terminal, subdomain 2 / Mycobacterial cell wall arabinan synthesis protein / EmbC C-terminal domain / Arabinosyltransferase concanavalin like domain / : ...arabinofuranosyltransferase like domain / Arabinofuranosyltransferase, central domain / Arabinofuranosyltransferase, domain 1 / Arabinosyltransferase, C-terminal / Arabinosyltransferas, concanavalin like domain / Arabinosyltransferase, C-terminal, subdomain 2 / Mycobacterial cell wall arabinan synthesis protein / EmbC C-terminal domain / Arabinosyltransferase concanavalin like domain / : / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-maltose / alpha-D-arabinofuranose / PHOSPHATE ION / Meromycolate extension acyl carrier protein / Probable arabinosyltransferase A / Integral membrane indolylacetylinositol arabinosyltransferase EmbC
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å
AuthorsZhao, Y. / Zhang, L. / Wu, L.J. / Wang, Q. / Li, J. / Besra, G.S. / Rao, Z.H.
Funding support China, United Kingdom, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFC0840300 China
National Science Foundation (NSF, China)81520108019 China
Chinese Academy of SciencesXDB29020000 China
Medical Research Council (MRC, United Kingdom)MR/S000542/1 United Kingdom
CitationJournal: Science / Year: 2020
Title: Structures of cell wall arabinosyltransferases with the anti-tuberculosis drug ethambutol.
Authors: Lu Zhang / Yao Zhao / Yan Gao / Lijie Wu / Ruogu Gao / Qi Zhang / Yinan Wang / Chengyao Wu / Fangyu Wu / Sudagar S Gurcha / Natacha Veerapen / Sarah M Batt / Wei Zhao / Ling Qin / Xiuna Yang ...Authors: Lu Zhang / Yao Zhao / Yan Gao / Lijie Wu / Ruogu Gao / Qi Zhang / Yinan Wang / Chengyao Wu / Fangyu Wu / Sudagar S Gurcha / Natacha Veerapen / Sarah M Batt / Wei Zhao / Ling Qin / Xiuna Yang / Manfu Wang / Yan Zhu / Bing Zhang / Lijun Bi / Xian'en Zhang / Haitao Yang / Luke W Guddat / Wenqing Xu / Quan Wang / Jun Li / Gurdyal S Besra / Zihe Rao /
Abstract: The arabinosyltransferases EmbA, EmbB, and EmbC are involved in cell wall synthesis and are recognized as targets for the anti-tuberculosis drug ethambutol. In this study, we determined cryo- ...The arabinosyltransferases EmbA, EmbB, and EmbC are involved in cell wall synthesis and are recognized as targets for the anti-tuberculosis drug ethambutol. In this study, we determined cryo-electron microscopy and x-ray crystal structures of mycobacterial EmbA-EmbB and EmbC-EmbC complexes in the presence of their glycosyl donor and acceptor substrates and with ethambutol. These structures show how the donor and acceptor substrates bind in the active site and how ethambutol inhibits arabinosyltransferases by binding to the same site as both substrates in EmbB and EmbC. Most drug-resistant mutations are located near the ethambutol binding site. Collectively, our work provides a structural basis for understanding the biochemical function and inhibition of arabinosyltransferases and the development of new anti-tuberculosis agents.
History
DepositionApr 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integral membrane indolylacetylinositol arabinosyltransferase EmbC
B: Integral membrane indolylacetylinositol arabinosyltransferase EmbC
C: Meromycolate extension acyl carrier protein
D: Meromycolate extension acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,97520
Polymers261,4874
Non-polymers3,48916
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.080, 176.330, 207.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Integral membrane indolylacetylinositol arabinosyltransferase EmbC / arabinosyltransferase EmbC


Mass: 119999.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: embC, MSMEI_6219
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: I7FMU5, UniProt: A0R612*PLUS, indolylacetylinositol arabinosyltransferase
#2: Protein Meromycolate extension acyl carrier protein / ACP


Mass: 10743.876 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R0B3

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Sugars , 3 types, 12 molecules

#3: Polysaccharide alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose


Type: oligosaccharide / Mass: 282.245 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DArafa1-5DArafa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a122h-1a_1-4]/1-1/a5-b1WURCSPDB2Glycan 1.1.0
[][a-D-Araf]{[(5+1)][a-D-Araf]{}}LINUCSPDB-CARE
#4: Polysaccharide
alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#7: Sugar
ChemComp-BXY / alpha-D-arabinofuranose / alpha-D-arabinose / D-arabinose / arabinose


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H10O5
IdentifierTypeProgram
DArafaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-arabinofuranoseCOMMON NAMEGMML 1.0
a-D-ArafIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 4 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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: 4.24 Å3/Da / Density % sol: 71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 50mM HEPES (pH 6.8~7.5), 100mM NaCl, 5-10% (v/v) polyethylene glycol 4000, 20-30% (v/v) polyethylene glycol 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→134.458 Å / Num. all: 67591 / Num. obs: 67591 / % possible obs: 99.9 % / Redundancy: 19.9 % / Rpim(I) all: 0.027 / Rrim(I) all: 0.118 / Rsym value: 0.114 / Net I/av σ(I): 1 / Net I/σ(I): 12.2 / Num. measured all: 1344351
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
3.3-3.4819.95.1760.119454197751.1845.3115.1760.7100
3.48-3.6920.22.7980.318620092400.6362.872.7981.3100
3.69-3.94211.3960.518187186790.3121.4311.3962.8100
3.94-4.2620.60.6371.216707681070.1440.6530.6375.9100
4.26-4.6719.80.3122.314871875090.0720.320.31210.8100
4.67-5.2220.10.1724.113688367950.0390.1770.17216.9100
5.22-6.0320.40.1434.912249260180.0320.1470.14320.4100
6.03-7.3818.40.0976.69446451370.0230.10.09728.7100
7.38-10.4418.30.057107372840360.0140.0590.05741.499.9
10.44-49.60316.70.0446774913837822950.0120.0460.0443837898.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.3→49.67 Å / Cor.coef. Fo:Fc: 0.788 / Cor.coef. Fo:Fc free: 0.73 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 5.608 / SU Rfree Blow DPI: 0.427
RfactorNum. reflection% reflectionSelection details
Rfree0.265 3362 4.98 %RANDOM
Rwork0.232 ---
obs0.234 67568 100 %-
Displacement parametersBiso max: 230.27 Å2 / Biso mean: 78.18 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-5.3329 Å20 Å20 Å2
2---1.4806 Å20 Å2
3----3.8522 Å2
Refine analyzeLuzzati coordinate error obs: 0.52 Å
Refinement stepCycle: final / Resolution: 3.3→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17088 0 228 0 17316
Biso mean--83.9 --
Num. residues----2238
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5692SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2916HARMONIC5
X-RAY DIFFRACTIONt_it17782HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2410SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact21559SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d17782HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg24382HARMONIC21.21
X-RAY DIFFRACTIONt_omega_torsion2.64
X-RAY DIFFRACTIONt_other_torsion22.3
LS refinement shellResolution: 3.3→3.39 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2566 235 4.75 %
Rwork0.2566 4717 -
all0.2566 4952 -
obs--100 %
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)
12.4264-0.44911.17452.4583-0.28431.91750.20080.9916-0.0092-0.80450.12950.24520.36460.2335-0.3303-0.34550.2425-0.2152-0.4095-0.3039-0.2994119.168199.13943.9775
22.96490.1334-0.80921.19940.42921.20690.0228-0.9739-0.55520.7130.56220.7931-0.3537-0.6812-0.585-0.4208-0.0182-0.3038-0.213-0.3005-0.4071106.724201.94685.2817
36.4121-3.1197-2.35513.6029-1.22170.16980.00820.1259-0.0781-0.0367-0.0451-0.146-0.11940.25640.0369-0.26370.2033-0.06070.3223-0.10760.0749173.21191.42757.8744
46.2280.2883.52073.2544-1.99514.6896-0.0824-0.1632-0.08330.0881-0.1913-0.09860.110.07060.2736-0.29030.0097-0.23330.3367-0.0696-0.0609158.691192.413104.74
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A10 - 1075
2X-RAY DIFFRACTION2{ B|* }B10 - 1075
3X-RAY DIFFRACTION3{ C|* }C3 - 86
4X-RAY DIFFRACTION4{ D|* }D3 - 86

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