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- PDB-1hm9: CRYSTAL STRUCTURE OF S.PNEUMONIAE N-ACETYLGLUCOSAMINE-1-PHOSPHATE... -

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Basic information

Entry
Database: PDB / ID: 1hm9
TitleCRYSTAL STRUCTURE OF S.PNEUMONIAE N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE, GLMU, BOUND TO ACETYL COENZYME A AND UDP-N-ACETYLGLUCOSAMINE
ComponentsUDP-N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE
KeywordsTRANSFERASE / ACETYLTRANSFERASE / BIFUNCTIONAL / DRUG DESIGN / PYROPHOSPHORYLASE / Rossmann-like fold / left-handed-beta-helix / trimer / domain-interchange
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 morphogenesis / cell wall organization / 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 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 / : / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Nucleotidyl transferase domain / Nucleotidyl transferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 ...Bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase / GlmU, C-terminal LbH domain / : / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Nucleotidyl transferase domain / Nucleotidyl transferase / 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
ACETYL COENZYME *A / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / Bifunctional protein GlmU
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSulzenbacher, G. / Gal, L. / Peneff, C. / Fassy, F. / Bourne, Y.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Crystal structure of Streptococcus pneumoniae N-acetylglucosamine-1-phosphate uridyltransferase bound to acetyl-coenzyme A reveals a novel active site architecture.
Authors: Sulzenbacher, G. / Gal, L. / Peneff, C. / Fassy, F. / Bourne, Y.
History
DepositionDec 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Sep 25, 2019Group: Data collection / Category: reflns_shell
Item: _reflns_shell.meanI_over_sigI_obs / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_Rsym_value
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: UDP-N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE
B: UDP-N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,23414
Polymers101,0792
Non-polymers3,15412
Water12,502694
1
A: UDP-N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE
hetero molecules

A: UDP-N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE
hetero molecules

A: UDP-N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,35121
Polymers151,6193
Non-polymers4,73218
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area21490 Å2
ΔGint-156 kcal/mol
Surface area48140 Å2
MethodPISA
2
B: UDP-N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE
hetero molecules

B: UDP-N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE
hetero molecules

B: UDP-N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,35121
Polymers151,6193
Non-polymers4,73218
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 area21510 Å2
ΔGint-153 kcal/mol
Surface area48250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.509, 89.509, 278.753
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Cell settingtrigonal
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-1904-

CA

21B-2904-

CA

31A-1056-

HOH

41A-1260-

HOH

51B-2035-

HOH

61B-2259-

HOH

71B-2295-

HOH

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Components

#1: Protein UDP-N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE / E.C.2.7.7.23 / GLMU


Mass: 50539.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: GLMU / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: Q97R46, UDP-N-acetylglucosamine diphosphorylase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#4: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 694 / 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: 2.13 Å3/Da / Density % sol: 42.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 18 % PEG 400 (w/w), 300 mM CaCl2 50 mM NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP at 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
113 mg/mlprotein1drop
226 %(v/v)PEG4001reservoir
350 mM1reservoirNaCl
4300 mM1reservoirCaCl2pH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD / Date: May 16, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 84013 / Num. obs: 82248 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Biso Wilson estimate: 18.37 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 12.3
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 2 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5926 / % possible all: 96.4
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 187478
Reflection shell
*PLUS
% possible obs: 96.4 % / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HM8

1hm8


Resolution: 1.75→29.14 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3784263.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.219 8308 10.1 %RANDOM
Rwork0.183 ---
all0.183 82248 --
obs0.183 82248 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.86 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso mean: 23.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å22.05 Å20 Å2
2--2.02 Å20 Å2
3----4.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.75→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6930 0 188 694 7812
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.53
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.6671.5
X-RAY DIFFRACTIONc_mcangle_it2.2872.5
X-RAY DIFFRACTIONc_scbond_it2.6942
X-RAY DIFFRACTIONc_scangle_it3.8563
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 1375 10.2 %
Rwork0.276 12162 -
obs--96.6 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2.5
X-RAY DIFFRACTIONc_scangle_it3
LS refinement shell
*PLUS
Rfactor Rfree: 0.312 / % reflection Rfree: 10.2 % / Rfactor Rwork: 0.276

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