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Basic information

Entry
Database: PDB / ID: 1g0r
TitleTHE STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND REGULATION OF GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE (RMLA). THYMIDINE/GLUCOSE-1-PHOSPHATE COMPLEX.
ComponentsGLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
KeywordsTRANSFERASE / L-rhamnose / nucleotidyltransferase / pyrophosphorylase / thymidylyltransferase / allostery
Function / homology
Function and homology information


glucose-1-phosphate thymidylyltransferase / glucose-1-phosphate thymidylyltransferase activity / dTDP-rhamnose biosynthetic process / lipopolysaccharide core region biosynthetic process / nucleotide binding / metal ion binding
Similarity search - Function
Glucose-1-phosphate thymidylyltransferase, short form / Nucleotidyl transferase domain / Nucleotidyl transferase / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
1-O-phosphono-alpha-D-glucopyranose / THYMIDINE / Glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.87 Å
AuthorsBlankenfeldt, W. / Asuncion, M. / Lam, J.S. / Naismith, J.H.
Citation
Journal: EMBO J. / Year: 2000
Title: The structural basis of the catalytic mechanism and regulation of glucose-1-phosphate thymidylyltransferase (RmlA).
Authors: Blankenfeldt, W. / Asuncion, M. / Lam, J.S. / Naismith, J.H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: The Purification, Crystallisation and Preliminary Structural Characterisation of Glucose-1-phosphate Thymidylyltransferase (RmlA), the First Enzyme of the dTDP-L-rhamnose Synthesis Pathway ...Title: The Purification, Crystallisation and Preliminary Structural Characterisation of Glucose-1-phosphate Thymidylyltransferase (RmlA), the First Enzyme of the dTDP-L-rhamnose Synthesis Pathway from Pseudomonas aeruginosa
Authors: Blankenfeldt, W. / Giraud, M.F. / Leonard, G. / Rahim, R. / Creuzenet, C. / Lam, J.S. / Naismith, J.H.
#2: Journal: J.Biol.Chem. / Year: 1965
Title: The Nucleotide Specificity and Feedback Control of Thymidine Diphosphate D-glucose Pyrophosphorylase
Authors: Melo, A. / Glaser, L.
History
DepositionOct 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
B: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
C: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
D: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
E: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
F: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
G: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
H: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,81754
Polymers259,9118
Non-polymers7,90646
Water40,2822236
1
A: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
B: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
C: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
D: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,08728
Polymers129,9554
Non-polymers4,13124
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
F: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
G: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
H: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,73026
Polymers129,9554
Non-polymers3,77522
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)71.274, 73.084, 133.652
Angle α, β, γ (deg.)89.98, 81.42, 81.56
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a tetramer that can be described as a dimer of dimers.

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Components

#1: Protein
GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE / GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE (RMLA)


Mass: 32488.844 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: PET23(+) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HU22, glucose-1-phosphate thymidylyltransferase
#2: Sugar
ChemComp-G1P / 1-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-1-PHOSPHATE / 1-O-phosphono-alpha-D-glucose / 1-O-phosphono-D-glucose / 1-O-phosphono-glucose


Type: D-saccharide / Mass: 260.136 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H14N2O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2236 / 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: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 9-11% (w/v) PEG 6000 0.5 M lithium sulfate cocrystallisation with ligands, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 293 K
Details: Blankenfeldt, W., (2000) Acta Crystallogr.,Sect.D, 56, 1501.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19-12 %(w/v)PEG60001reservoir
20.5 Mlithium sulfate1reservoir
30.1 Mcitrate/NaOH1reservoiror are

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 29, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.87→72.55 Å / Num. obs: 183207 / % possible obs: 84.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 6.9
Reflection shellResolution: 1.87→1.97 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.291 / % possible all: 66.8
Reflection
*PLUS
Num. measured all: 333697
Reflection shell
*PLUS
% possible obs: 66.8 % / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 1.87→73 Å / SU B: 10.81297 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.21113 / Stereochemistry target values: Engh & Huber
Details: Initial TLS-refinement. Anisotropic B-values calculated but not refined
RfactorNum. reflection% reflectionSelection details
Rfree0.221 9145 5 %RANDOM
Rwork0.147 ---
obs0.151 174042 84 %-
Displacement parametersBiso mean: 17.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å2-0.01 Å20.71 Å2
2--0.7 Å20.2 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.87→73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18288 0 499 2236 21023
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.021
X-RAY DIFFRACTIONp_mcbond_it2.0971.5
X-RAY DIFFRACTIONp_mcangle_it2.6742
X-RAY DIFFRACTIONp_scbond_it5.2843
X-RAY DIFFRACTIONp_scangle_it6.1144.5
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.1510.2
Software
*PLUS
Name: REFMAC5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.52
LS refinement shell
*PLUS
Rfactor Rfree: 0.395 / Rfactor Rwork: 0.232

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