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- PDB-4mvc: Crystal Structure of a Mammalian Cytidylyltransferase -

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Basic information

Entry
Database: PDB / ID: 4mvc
TitleCrystal Structure of a Mammalian Cytidylyltransferase
ComponentsCholine-phosphate cytidylyltransferase A
KeywordsTRANSFERASE / Rossmann Fold / Amphipathic helix / Lipid Membrane Binding / Cytidine 5 -diphosphocholine synthesis / Phosphatidylcholine homeostasis / Lipid Membrane Surface / Endoplasmic Reticulum / Nucleus
Function / homology
Function and homology information


Synthesis of PC / choline-phosphate cytidylyltransferase / choline-phosphate cytidylyltransferase activity / CDP-choline pathway / glycogen granule / phosphatidylcholine biosynthetic process / phosphatidylcholine binding / extrinsic component of membrane / molecular function inhibitor activity / nuclear envelope ...Synthesis of PC / choline-phosphate cytidylyltransferase / choline-phosphate cytidylyltransferase activity / CDP-choline pathway / glycogen granule / phosphatidylcholine biosynthetic process / phosphatidylcholine binding / extrinsic component of membrane / molecular function inhibitor activity / nuclear envelope / calmodulin binding / lipid binding / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / identical protein binding / nucleus / cytosol
Similarity search - Function
Choline-phosphate cytidylyltransferase Pcy1-like / CTP:phosphocholine cytidylyltransferase domain / Cytidylyltransferase-like / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CDC / Choline-phosphate cytidylyltransferase A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLee, J. / Cornell, R.B.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural Basis for Autoinhibition of CTP:Phosphocholine Cytidylyltransferase (CCT), the Regulatory Enzyme in Phosphatidylcholine Synthesis, by Its Membrane-binding Amphipathic Helix.
Authors: Lee, J. / Taneva, S.G. / Holland, B.W. / Tieleman, D.P. / Cornell, R.B.
History
DepositionSep 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Choline-phosphate cytidylyltransferase A
B: Choline-phosphate cytidylyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1924
Polymers68,2152
Non-polymers9772
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-39 kcal/mol
Surface area17850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.260, 44.550, 97.130
Angle α, β, γ (deg.)90.00, 111.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Choline-phosphate cytidylyltransferase A / CCT-alpha / CTP:phosphocholine cytidylyltransferase A / CCT A / CT A / Phosphorylcholine transferase A


Mass: 34107.441 Da / Num. of mol.: 2 / Fragment: CCT1-312 (del 238-269) / Mutation: Deletions (238-269) and (313-367)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ctpct, Pcyt1, Pcyt1a / Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta BL21(DE3)
References: UniProt: P19836, choline-phosphate cytidylyltransferase
#2: Chemical ChemComp-CDC / [2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM / Citicoline


Mass: 488.324 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H26N4O11P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris (pH 8.5), 20% PEG 10,000, 0.2 M sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 8, 2013 / Details: collimating mirror with two stripes (Si, Rh/Pt)
RadiationMonochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 14192 / Num. obs: 13085 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 44.168 Å2 / Rmerge(I) obs: 0.141 / Net I/σ(I): 7
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1901 / % possible all: 92.3

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Processing

Software
NameVersionClassification
MXData Collectordata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HL4

3hl4


Resolution: 3→39.974 Å / SU ML: 0.79 / σ(F): 1.36 / Phase error: 29.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2878 649 4.97 %RANDOM
Rwork0.2229 ---
obs0.2262 13068 91.12 %-
all-14342 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.697 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.7285 Å2-0 Å2-3.3664 Å2
2---16.7635 Å20 Å2
3---27.492 Å2
Refinement stepCycle: LAST / Resolution: 3→39.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3113 0 62 19 3194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043261
X-RAY DIFFRACTIONf_angle_d0.9584462
X-RAY DIFFRACTIONf_dihedral_angle_d16.2351120
X-RAY DIFFRACTIONf_chiral_restr0.062493
X-RAY DIFFRACTIONf_plane_restr0.004576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.23160.32271420.2562457X-RAY DIFFRACTION91
3.2316-3.55670.29191220.21852444X-RAY DIFFRACTION91
3.5567-4.07090.27291270.19212484X-RAY DIFFRACTION91
4.0709-5.12720.27981260.20232470X-RAY DIFFRACTION91
5.1272-39.97750.28381320.25612564X-RAY DIFFRACTION91

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