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- PDB-1g2v: THE STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND REGULATION OF... -

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Basic information

Entry
Database: PDB / ID: 1g2v
TitleTHE STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND REGULATION OF GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE (RMLA). TTP 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
THYMIDINE-5'-TRIPHOSPHATE / Glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.6 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 21, 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 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 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)267,62524
Polymers259,9118
Non-polymers7,71516
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)133,81312
Polymers129,9554
Non-polymers3,8578
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18910 Å2
ΔGint-78 kcal/mol
Surface area41620 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)133,81312
Polymers129,9554
Non-polymers3,8578
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18940 Å2
ΔGint-81 kcal/mol
Surface area41560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.017, 134.361, 140.901
Angle α, β, γ (deg.)90.00, 98.22, 90.00
Int Tables number4
Space group name H-MP1211

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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: PET23A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(LAMBDA DE3)
References: UniProt: Q9HU22, glucose-1-phosphate thymidylyltransferase
#2: Chemical
ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H17N2O14P3

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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: 2.53 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 5% (w/v) PEG 6000, 0.1 M Na-citrate pH 4.0; protein incubated with 10 mM dTTP, pH 4.00, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 %(w/v)PEG60001reservoir
20.1 MNa citrate1reservoir
325 %(v/v)PEG6001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jul 31, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 7557 / % possible obs: 91.5 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 42.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.4
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3 % / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 4.6 / % possible all: 60.1
Reflection
*PLUS
Num. obs: 75557 / Num. measured all: 310827
Reflection shell
*PLUS
% possible obs: 60.1 %

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementStarting model: 1G1L

1g1l


Resolution: 2.6→100 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.37
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3797 5 %RANDOM
Rwork0.215 ---
obs0.217 71748 91.4 %-
Displacement parametersBiso mean: 13.16 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å20 Å20.08 Å2
2---0.03 Å20 Å2
3---1.36 Å2
Refinement stepCycle: LAST / Resolution: 2.6→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18280 0 464 0 18744
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0280.021
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.7641.5
X-RAY DIFFRACTIONp_mcangle_it1.5892
X-RAY DIFFRACTIONp_scbond_it3.0133
X-RAY DIFFRACTIONp_scangle_it4.9634.5
X-RAY DIFFRACTIONp_plane_restr0.0090.02
X-RAY DIFFRACTIONp_chiral_restr0.120.2
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
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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