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- PDB-2v0l: Characterization of Substrate Binding and Catalysis of the Potent... -

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Entry
Database: PDB / ID: 2v0l
TitleCharacterization of Substrate Binding and Catalysis of the Potential Antibacterial Target N-acetylglucosamine-1-phosphate Uridyltransferase (GlmU)
ComponentsBIFUNCTIONAL PROTEIN GLMU
KeywordsTRANSFERASE / GLMU / CELL WALL / MAGNESIUM / CELL SHAPE / PEPTIDOGLYCAN SYNTHESIS / MULTIFUNCTIONAL ENZYME / NUCLEOTIDYLTRANSFERASE / URIDYLATION / METAL-BINDING / ACYLTRANSFERASE / CATALYTIC MECHANISM / ASSOCIATIVE MECHANISM
Function / homology
Function and homology information


glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / cell morphogenesis / regulation of cell shape ...glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / cell morphogenesis / regulation of cell shape / magnesium ion binding / membrane / 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 transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 ...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 transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 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
TRIETHYLENE GLYCOL / URIDINE / Bifunctional protein GlmU
Similarity search - Component
Biological speciesHAEMOPHILUS INFLUENZAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMochalkin, I. / Lightle, S. / Ohren, J.F. / Chirgadze, N.Y.
CitationJournal: Protein Sci. / Year: 2007
Title: Characterization of Substrate Binding and Catalysis in the Potential Antibacterial Target N-Acetylglucosamine-1-Phosphate Uridyltransferase (Glmu).
Authors: Mochalkin, I. / Lightle, S. / Zhu, Y. / Ohren, J.F. / Spessard, C. / Chirgadze, N.Y. / Banotai, C. / Melnick, M. / Mcdowell, L.
History
DepositionMay 14, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BIFUNCTIONAL PROTEIN GLMU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,75712
Polymers49,3461
Non-polymers1,41111
Water7,422412
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)152,27236
Polymers148,0383
Non-polymers4,23433
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 area15500 Å2
ΔGint-58.8 kcal/mol
Surface area65490 Å2
MethodPQS
Unit cell
Length a, b, c (Å)108.720, 108.720, 326.754
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein , 1 types, 1 molecules A

#1: Protein BIFUNCTIONAL PROTEIN GLMU / GLMU FROM HAEMOPHILUS INFLUENZAE


Mass: 49346.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HAEMOPHILUS INFLUENZAE (bacteria) / References: UniProt: P43889, Transferases

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Non-polymers , 5 types, 423 molecules

#2: Chemical ChemComp-URI / URIDINE


Mass: 244.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N2O6
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 3.38 Å3/Da / Density % sol: 63.33 % / Description: NONE
Crystal growpH: 6 / Details: pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 38714 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 27.7
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.25 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V0H

2v0h


Resolution: 2.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rwork0.187 ---
obs-38714 99.9 %-
Rfree---0.233
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3415 0 85 412 3912

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