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- PDB-7mpk: Crystal structure of TagA with UDP-GlcNAc -

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Basic information

Entry
Database: PDB / ID: 7mpk
TitleCrystal structure of TagA with UDP-GlcNAc
ComponentsN-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / WALL TEICHOIC ACID ENZYME / BETA-N-2 ACETYLMANNOSAMINYLTRANSFERASE / UDP-N-ACETYLGLUCOSAMINE
Function / homology
Function and homology information


N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase / N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase activity / teichoic acid biosynthetic process / cell wall organization / nucleotide binding
Similarity search - Function
Glycosyl transferase WecG/TagA/CpsF / N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase / Glycosyl transferase WecG/TagA/CpsF family
Similarity search - Domain/homology
URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
Similarity search - Component
Biological speciesThermoanaerobacter italicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.993 Å
AuthorsMartinez, O.E. / Cascio, D. / Clubb, R.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI52217 United States
Department of Energy (DOE, United States)DE-FC0 2-02ER63421 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Insight into the molecular basis of substrate recognition by the wall teichoic acid glycosyltransferase TagA.
Authors: Martinez, O.E. / Mahoney, B.J. / Goring, A.K. / Yi, S.W. / Tran, D.P. / Cascio, D. / Phillips, M.L. / Muthana, M.M. / Chen, X. / Jung, M.E. / Loo, J.A. / Clubb, R.T.
History
DepositionMay 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
B: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
C: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5426
Polymers83,7203
Non-polymers1,8223
Water362
1
A: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5142
Polymers27,9071
Non-polymers6071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5142
Polymers27,9071
Non-polymers6071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5142
Polymers27,9071
Non-polymers6071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.240, 113.240, 114.450
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase / N-acetylmannosaminyltransferase / UDP-N-acetylmannosamine transferase / UDP-N-acetylmannosamine:N- ...N-acetylmannosaminyltransferase / UDP-N-acetylmannosamine transferase / UDP-N-acetylmannosamine:N-acetylglucosaminyl pyrophosphorylundecaprenol N-acetylmannosaminyltransferase


Mass: 27906.801 Da / Num. of mol.: 3 / Mutation: C111A, I203E, L209Q, L212K, I216E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter italicus (strain DSM 9252 / Ab9) (bacteria)
Strain: DSM 9252 / Ab9 / Gene: Thit_1850 / Plasmid: pMAPLe4 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: D3T4E0, N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
#2: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 3 / Fragment: UD1 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% PEG-8000, 8% ethylene glycol, 0.1M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9797 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.99→74.47 Å / Num. obs: 17473 / % possible obs: 99.7 % / Redundancy: 9.804 % / Biso Wilson estimate: 106.31 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.12 / Χ2: 0.911 / Net I/σ(I): 16.47 / Num. measured all: 171310 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.99-3.078.9910.833.3311176128812430.8580.88196.5
3.07-3.168.9140.624.5110982123312320.9230.65999.9
3.16-3.2510.2540.486.1812377120712070.9560.506100
3.25-3.3510.4140.3797.7812288118011800.970.399100
3.35-3.4610.3010.27510.0711537112011200.9830.29100
3.46-3.5810.2640.23212.0111516112211220.9890.245100
3.58-3.7110.1750.18614.9710714105310530.9910.196100
3.71-3.869.9750.15416.710414104410440.9930.162100
3.86-4.049.5980.12918.9295319939930.9940.136100
4.04-4.239.2230.10220.9387349489470.9960.10899.9
4.23-4.4610.3530.09423.5893809069060.9960.1100
4.46-4.7310.3330.08525.2789078628620.9970.089100
4.73-5.0610.1790.08525.5481337997990.9970.09100
5.06-5.479.7840.09123.4673877557550.9960.096100
5.47-5.999.2450.08923.3265367077070.9960.094100
5.99-6.699.4980.0824.7660696416390.9960.08599.7
6.69-7.7310.0040.0728.9855825585580.9980.074100
7.73-9.479.6730.05931.9247984964960.9980.062100
9.47-13.398.3790.05431.2331843803800.9980.058100
13.39-74.478.9780.05532.6820652312300.9990.05899.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.99 Å74.47 Å
Translation2.99 Å74.47 Å

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Processing

Software
NameVersionClassification
BUSTERrefinement
XSCALE20190315data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.27data extraction
XDS20190315data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WB4

5wb4


Resolution: 2.993→74.47 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.864 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.393
RfactorNum. reflection% reflectionSelection details
Rfree0.2574 1748 10 %RANDOM
Rwork0.2042 ---
obs0.2094 17473 99.7 %-
Displacement parametersBiso max: 122.08 Å2 / Biso mean: 71.18 Å2 / Biso min: 48.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.0103 Å20 Å20 Å2
2---0.0103 Å20 Å2
3---0.0205 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: final / Resolution: 2.993→74.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4519 0 234 2 4755
Biso mean--66.4 54.05 -
Num. residues----592
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1744SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes797HARMONIC5
X-RAY DIFFRACTIONt_it4840HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion628SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies3HARMONIC1
X-RAY DIFFRACTIONt_utility_distance19HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3636SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4840HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg6581HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion2.35
X-RAY DIFFRACTIONt_other_torsion20.94
LS refinement shellResolution: 2.993→3.02 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.521 35 10 %
Rwork0.2984 315 -
obs--88.31 %
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)
11.70230.74690.17812.54680.69041.1834-0.03960.0319-0.0431-0.45770.2321-0.0717-0.3153-0.0694-0.19240.1586-0.10240.0177-0.10590.0286-0.127617.0345-34.2857-2.1779
21.7555-1.7984-0.2662.94140.85222.2110.13120.07510.3759-0.25830.0449-0.579-0.3350.4883-0.1762-0.111-0.23150.0887-0.0089-0.01610.085237.0109-71.4289-16.3451
31.69230.5352-0.92052.321-0.19822.842-0.09510.0726-0.15140.1867-0.08750.2785-0.0523-0.17530.1827-0.0366-0.11450.0352-0.0822-0.081-0.0084-1.614-73.2674-0.0663
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 198
2X-RAY DIFFRACTION2{ B|* }B2 - 199
3X-RAY DIFFRACTION3{ C|* }C1 - 197

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