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- PDB-8v33: Crystal structure of S. aureus TarL N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 8v33
TitleCrystal structure of S. aureus TarL N-terminal domain
ComponentsTeichoic acid ribitol-phosphate polymerase TarL
KeywordsTRANSFERASE / glycosyltransferase / immunoglobulin-like domain
Function / homology
Function and homology information


CDP-ribitol ribitolphosphotransferase / CDP-ribitol ribitolphosphotransferase activity / CDP-glycerol glycerophosphotransferase activity / teichoic acid biosynthetic process / cell wall organization / plasma membrane
Similarity search - Function
: / CDP-glycerol glycerophosphotransferase / CDP-glycerol glycerophosphotransferase, C-terminal domain / CDP-glycerol glycerophosphotransferase, N-terminal domain / CDP-Glycerol:Poly(glycerophosphate) glycerophosphotransferase
Similarity search - Domain/homology
SUCCINIC ACID / Teichoic acid ribitol-phosphate polymerase TarL
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLi, F.K.K. / Strynadka, N.C.J.
Funding support Canada, United States, 4items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
Canadian Institutes of Health Research (CIHR) Canada
Howard Hughes Medical Institute (HHMI) United States
Canada Research Chairs Canada
CitationJournal: Sci Adv / Year: 2024
Title: Cryo-EM analysis of TarL, a polymerase in wall teichoic acid biogenesis central to virulence and antibiotic resistance.
Authors: Franco K K Li / Liam J Worrall / Robert T Gale / Eric D Brown / Natalie C J Strynadka /
Abstract: Wall teichoic acid (WTA), a covalent adduct of Gram-positive bacterial cell wall peptidoglycan, contributes directly to virulence and antibiotic resistance in pathogenic species. Polymerization of ...Wall teichoic acid (WTA), a covalent adduct of Gram-positive bacterial cell wall peptidoglycan, contributes directly to virulence and antibiotic resistance in pathogenic species. Polymerization of the WTA ribitol-phosphate chain is catalyzed by TarL, a member of the largely uncharacterized TagF-like family of membrane-associated enzymes. We report the cryo-electron microscopy structure of TarL, showing a tetramer that forms an extensive membrane-binding platform of monotopic helices. TarL is composed of an amino-terminal immunoglobulin-like domain and a carboxyl-terminal glycosyltransferase-B domain for ribitol-phosphate polymerization. The active site of the latter is complexed to donor substrate cytidine diphosphate-ribitol, providing mechanistic insights into the catalyzed phosphotransfer reaction. Furthermore, the active site is surrounded by electropositive residues that serve to retain the lipid-linked acceptor for polymerization. Our data advance general insight into the architecture and membrane association of the still poorly characterized monotopic membrane protein class and present molecular details of ribitol-phosphate polymerization that may aid in the design of new antimicrobials.
History
DepositionNov 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Teichoic acid ribitol-phosphate polymerase TarL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3122
Polymers22,1941
Non-polymers1181
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.634, 69.634, 66.590
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-310-

HOH

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Components

#1: Protein Teichoic acid ribitol-phosphate polymerase TarL


Mass: 22193.793 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: tarL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2G1B8
#2: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.8 M succinic acid pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.7→44.7 Å / Num. obs: 20949 / % possible obs: 99.95 % / Redundancy: 39.6 % / Biso Wilson estimate: 24.79 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 24.6
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 2.02 % / Mean I/σ(I) obs: 2.02 / Num. unique obs: 2053 / CC1/2: 0.718 / CC star: 0.914 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→44.7 Å / SU ML: 0.2273 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.9898
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2206 1218 5.82 %
Rwork0.1802 19722 -
obs0.1825 20940 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.83 Å2
Refinement stepCycle: LAST / Resolution: 1.7→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1314 0 8 143 1465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00881343
X-RAY DIFFRACTIONf_angle_d1.08791821
X-RAY DIFFRACTIONf_chiral_restr0.0791207
X-RAY DIFFRACTIONf_plane_restr0.0081238
X-RAY DIFFRACTIONf_dihedral_angle_d5.9627175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.770.33751310.27752161X-RAY DIFFRACTION100
1.77-1.850.27991350.23082162X-RAY DIFFRACTION100
1.85-1.950.2611310.21892158X-RAY DIFFRACTION100
1.95-2.070.251350.19382156X-RAY DIFFRACTION99.91
2.07-2.230.22721350.18552187X-RAY DIFFRACTION99.96
2.23-2.450.21431350.18212186X-RAY DIFFRACTION99.96
2.45-2.810.22411370.18672186X-RAY DIFFRACTION100
2.81-3.540.20191370.17592215X-RAY DIFFRACTION99.96
3.54-44.70.20311420.15742311X-RAY DIFFRACTION99.88
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)
14.732121391833.11239995032-1.647855980334.34830867633-0.6358965613151.92788515319-0.1764904639930.0480180425712-0.252274042152-0.05628323653720.0317270396992-0.1710768229190.1687288933320.04580180005890.08566067553140.1496917221710.007623450194690.0003827784734090.151351612055-0.007479880133430.16550187318545.38294185027.7481142882220.477031767
26.6579268877-4.38683648398-4.956002024855.482365097385.029293773086.854531307510.132487976127-0.4233937274930.3619143158670.1844995444430.0870719078211-0.2828545743260.01219370567610.388013185688-0.2432196599060.191302594768-0.0416494999391-0.003292338258810.170303302939-0.01548397672890.18885678441538.686785397813.257546703533.9313527016
35.718464191731.15158601978-4.028535858274.12622677052-1.67029129213.98158613415-0.4883013025250.020514720915-0.351686938932-0.2239277215880.0287354177401-0.4402605336130.591178067320.2512960968920.4051375078820.2094678895520.0161800365667-0.01192678124330.2260800634460.03381612125540.26235143643546.69854850762.8855955465226.7581689781
43.58528197483-0.0293423875499-1.661376195762.04815301690.3041698156591.87570515388-0.113419691387-0.168808210128-0.06872193448770.09187756041660.0540797038602-0.02998133031260.03392224615330.1334558642850.08274490675750.187113937739-0.00657567620036-0.008658199227380.1683410413790.006053197798790.14856321498736.88634710135.1425660556730.5029131827
56.380939103151.994077218175.203408328751.818112234482.148841192458.65924193306-0.05686473183660.460477293306-0.0584122671944-0.1814144510550.183639365361-0.095337469775-0.1465003306560.761324766048-0.1668787287690.1952654857640.003527363357950.01513240931660.183590653912-0.02488643577980.18373847397641.367122195513.408468498216.9460009735
68.89365906839-1.49603401594-0.4257422799191.981217960911.276454894675.553991066890.2898347492080.571887840745-0.774393876845-0.39747222419-0.4182559304410.7922670558030.374673998088-1.341801700410.1125354545410.286003031508-0.0472322492454-0.03872143568160.531493521198-0.03945722329220.35331043352221.844442113411.05748655565.47536915993
75.158055217870.347397755176-0.5468721549299.65903659719-1.678231416935.943514935470.138891456096-0.1213420677640.4693791455140.0988117581052-0.09130854958980.326470120282-0.310440205589-0.453811783197-0.03992545220330.1756658959020.01064830565610.002983039178620.284022930768-0.03808106472220.19769147916727.110464199617.004064831612.0184861511
82.398868210371.86237701376-1.030497151365.78589109803-1.234158553343.09996673428-0.1174514505970.1390519444760.103604720989-0.0329601911170.2297858999970.3261564066220.101512887169-0.334366384852-0.1246278892480.19787537131-0.0277813280623-0.004214215805940.237340801016-0.0008957591153080.21390290755326.96222773719.6096397299425.6369374525
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 33 )1 - 331 - 33
22chain 'A' and (resid 34 through 43 )34 - 4334 - 43
33chain 'A' and (resid 44 through 55 )44 - 5544 - 55
44chain 'A' and (resid 56 through 82 )56 - 8256 - 82
55chain 'A' and (resid 83 through 101 )83 - 10183 - 101
66chain 'A' and (resid 102 through 113 )102 - 113102 - 113
77chain 'A' and (resid 114 through 128 )114 - 128114 - 128
88chain 'A' and (resid 129 through 164 )129 - 164129 - 159

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