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- PDB-3dj4: Crystal Structure of GlmU from Mycobacterium tuberculosis in comp... -

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Basic information

Entry
Database: PDB / ID: 3dj4
TitleCrystal Structure of GlmU from Mycobacterium tuberculosis in complex with URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE.
ComponentsBifunctional protein glmU
KeywordsTRANSFERASE / ACETYLTRANSFERASE / BIFUNCTIONAL / PYROPHOSPHORYLASE / ROSSMANN-LIKE FOLD / LEFT-HANDED-BETA-HELIX / TRIMER / Cell shape / Cell wall biogenesis/degradation / Cytoplasm / Magnesium / Metal-binding / Multifunctional enzyme / Nucleotidyltransferase / Peptidoglycan synthesis / Acyltransferase
Function / homology
Function and homology information


uridylyltransferase activity / adhesion of symbiont to host cell / glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / entry of bacterium into host cell / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process ...uridylyltransferase activity / adhesion of symbiont to host cell / glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / entry of bacterium into host cell / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell morphogenesis / cell wall organization / regulation of cell shape / magnesium ion binding / cytoplasm
Similarity search - Function
Bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase / GlmU, C-terminal LbH domain / MobA-like NTP transferase / MobA-like NTP transferase domain / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid ...Bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase / GlmU, C-terminal LbH domain / MobA-like NTP transferase / MobA-like NTP transferase domain / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / Bifunctional protein GlmU / Bifunctional protein GlmU
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.38 Å
AuthorsVerma, S.K. / Prakash, B.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: PknB-mediated phosphorylation of a novel substrate, N-acetylglucosamine-1-phosphate uridyltransferase, modulates its acetyltransferase activity.
Authors: Parikh, A. / Verma, S.K. / Khan, S. / Prakash, B. / Nandicoori, V.K.
History
DepositionJun 22, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional protein glmU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3284
Polymers51,6381
Non-polymers6913
Water2,648147
1
A: Bifunctional protein glmU
hetero molecules

A: Bifunctional protein glmU
hetero molecules

A: Bifunctional protein glmU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,98512
Polymers154,9133
Non-polymers2,0729
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area16750 Å2
ΔGint-183 kcal/mol
Surface area50520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.600, 78.600, 278.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-4048-

HOH

21A-4093-

HOH

31A-4121-

HOH

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Components

#1: Protein Bifunctional protein glmU / UDP-N-acetylglucosamine pyrophosphorylase / N-acetylglucosamine-1-phosphate uridyltransferase / ...UDP-N-acetylglucosamine pyrophosphorylase / N-acetylglucosamine-1-phosphate uridyltransferase / Glucosamine-1-phosphate N-acetyltransferase


Mass: 51637.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: glmU, Rv1018c, MT1046 / Plasmid: pQEII / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
References: UniProt: P96382, UniProt: P9WMN3*PLUS, UDP-N-acetylglucosamine diphosphorylase, glucosamine-1-phosphate N-acetyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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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: 3.2 Å3/Da / Density % sol: 61.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 8% PEG 8000, 150mM NaCl, 2mM MnCl2, 5% Glycerol, 1,3-butanediol, AMPPNP, MgCl2, DTT, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionHighest resolution: 2.38 Å / Num. obs: 25334 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 31.363 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 19.84
Reflection shellResolution: 2.38→2.44 Å / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 4.3 / Num. measured obs: 8246 / Num. unique obs: 1553 / % possible all: 82.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
RefinementResolution: 2.38→29.03 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.876 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.838 / SU B: 6.945 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.283 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1267 5 %RANDOM
Rwork0.194 ---
obs0.197 25333 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.59 Å2 / Biso mean: 24.694 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20.43 Å20 Å2
2--0.86 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 2.38→29.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3374 0 41 147 3562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0213473
X-RAY DIFFRACTIONr_angle_refined_deg2.5441.9714758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4675460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.11623.456136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.84915517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2141529
X-RAY DIFFRACTIONr_chiral_restr0.1370.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022603
X-RAY DIFFRACTIONr_nbd_refined0.2470.21486
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22270
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2158
X-RAY DIFFRACTIONr_metal_ion_refined0.0070.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.213
X-RAY DIFFRACTIONr_mcbond_it1.2861.52358
X-RAY DIFFRACTIONr_mcangle_it2.12523680
X-RAY DIFFRACTIONr_scbond_it3.57431247
X-RAY DIFFRACTIONr_scangle_it5.4574.51076
LS refinement shellResolution: 2.377→2.439 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 77 -
Rwork0.231 1466 -
all-1543 -
obs--100 %

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