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- PDB-1g23: THE STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND REGULATION OF... -

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Basic information

Entry
Database: PDB / ID: 1g23
TitleTHE STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND REGULATION OF GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE (RMLA). 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 / Glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 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 16, 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: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)264,74129
Polymers261,4118
Non-polymers3,33021
Water00
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)132,22713
Polymers130,7064
Non-polymers1,5219
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15330 Å2
ΔGint-143 kcal/mol
Surface area43220 Å2
MethodPISA
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)132,51516
Polymers130,7064
Non-polymers1,80912
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16020 Å2
ΔGint-178 kcal/mol
Surface area43110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.583, 73.901, 133.748
Angle α, β, γ (deg.)89.81, 80.31, 80.18
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a tetramer best described as a dimer of dimers.

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Components

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


Mass: 32676.422 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: PET23A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(LAMBDA DE3)
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.: 8
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.: 13 / Source method: obtained synthetically / Formula: SO4
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.17 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 9-11 % (w/v) PEG 6000, 0.5 M Li-sulfate, 0.1 M Na-citrate, 4+4 mikrolitre + 1 mikrolitre 100 mM G1P, 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-ID
19-12 %(w/v)PEG60001reservoir
20.5 Mlithium sulfate1reservoir
30.1 Mcitrate/NaOH1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.885 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 1, 2000
RadiationMonochromator: Si 111 Channel Cut Monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 121112 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 49 Å2 / Rmerge(I) obs: 0.024 / Net I/σ(I): 29.7
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.089 / Mean I/σ(I) obs: 9.8 / % possible all: 69.4
Reflection
*PLUS
Num. measured all: 224654
Reflection shell
*PLUS
% possible obs: 69.4 %

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2.8→72.55 Å / SU B: 19.9 / SU ML: 0.40774 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.50849 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 3103 5 %RANDOM
Rwork0.199 ---
obs0.2011 58982 95.1 %-
Displacement parametersBiso mean: 27.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.02 Å20.15 Å2
2--0.28 Å2-0.35 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.8→72.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18280 0 193 0 18473
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0250.021
X-RAY DIFFRACTIONp_mcbond_it0.8571.5
X-RAY DIFFRACTIONp_mcangle_it1.6642
X-RAY DIFFRACTIONp_scbond_it1.9353
X-RAY DIFFRACTIONp_scangle_it3.4964.5
X-RAY DIFFRACTIONp_plane_restr0.0070.02
X-RAY DIFFRACTIONp_chiral_restr0.1180.2
LS refinement shellResolution: 2.8→2.87 Å /
Rfactor% reflection
Rfree0.287 -
Rwork0.232 -
obs-69.4 %
Software
*PLUS
Name: REFMAC5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.27

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