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- PDB-2be9: Crystal structure of the CTP-liganded (T-State) aspartate transca... -

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Basic information

Entry
Database: PDB / ID: 2be9
TitleCrystal structure of the CTP-liganded (T-State) aspartate transcarbamoylase from the extremely thermophilic archaeon Sulfolobus acidocaldarius
Components
  • Aspartate carbamoyltransferase regulatory chain
  • Aspartate carbamoyltransferase
KeywordsTRANSFERASE / ATCASE / HYPERTHERMOPHILIC / TEMPERATURE / ALLOSTERIC / HOLOENZYME / CTP COMPLEX
Function / homology
Function and homology information


aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / metal ion binding
Similarity search - Function
Aspartate transcarbamylase regulatory subunit / Aspartate carbamoyltransferase regulatory subunit, C-terminal / Aspartate carbamoyltransferase regulatory subunit, N-terminal / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain superfamily / Aspartate carbamoyltransferase regulatory chain, allosteric domain / Aspartate carbamoyltransferase regulatory chain, metal binding domain / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain / Aspartate/ornithine carbamoyltransferase ...Aspartate transcarbamylase regulatory subunit / Aspartate carbamoyltransferase regulatory subunit, C-terminal / Aspartate carbamoyltransferase regulatory subunit, N-terminal / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain superfamily / Aspartate carbamoyltransferase regulatory chain, allosteric domain / Aspartate carbamoyltransferase regulatory chain, metal binding domain / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain / Aspartate/ornithine carbamoyltransferase / Aspartate carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / SH3 type barrels. / Roll / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-TRIPHOSPHATE / Aspartate carbamoyltransferase regulatory chain / Aspartate carbamoyltransferase catalytic subunit
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDe Vos, D. / Savvides, S.N. / Van Beeumen, J.J.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2008
Title: Crystal structure of Sulfolobus acidocaldarius aspartate carbamoyltransferase in complex with its allosteric activator CTP.
Authors: De Vos, D. / Xu, Y. / Aerts, T. / Van Petegem, F. / Van Beeumen, J.J.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: Crystal Structure of T State Aspartate Carbamoyltransferase of the Hyperthermophilic Archaeon Sulfolobus Acidocaldarius.
Authors: De Vos, D. / Van Petegem, F. / Remaut, H. / Legrain, C. / Glandorff, N. / Van Beeumen, J.
History
DepositionOct 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 23, 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 / diffrn_source / pdbx_initial_refinement_model / struct_conn / 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 / _diffrn_source.pdbx_synchrotron_site / _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.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_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

Downloads & links

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Assembly

Deposited unit
A: Aspartate carbamoyltransferase
B: Aspartate carbamoyltransferase regulatory chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8225
Polymers53,1782
Non-polymers6453
Water1,38777
1
A: Aspartate carbamoyltransferase
B: Aspartate carbamoyltransferase regulatory chain
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)322,93430
Polymers319,06612
Non-polymers3,86818
Water21612
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
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area30230 Å2
ΔGint-192 kcal/mol
Surface area105710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)131.932, 131.932, 139.132
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
DetailsThe biological assembly is a dodecamer generated from the heterodimer in the asymmetric unit by the operations: (-y,x-y,z);(-x+y,-x,z);(-y,-x,-z+1/2);(-x+y,y,-z+1/2);(x,x-y,-z+1/2)

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Aspartate carbamoyltransferase / / Aspartate transcarbamylase / ATCase


Mass: 34332.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: pyrB / Plasmid: pTrc99 / Production host: Escherichia coli (E. coli) / Strain (production host): C600(delta(pyrBI) / References: UniProt: Q55338, aspartate carbamoyltransferase
#2: Protein Aspartate carbamoyltransferase regulatory chain


Mass: 18845.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: pyrI / Plasmid: pTrc99 / Production host: Escherichia coli (E. coli) / Strain (production host): C600(delta(pyrBI) / References: UniProt: P74766

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Non-polymers , 4 types, 80 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.29 Å3/Da / Density % sol: 62.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: AMMONIUM SULFATE, SODIUM ACETATE CTP soak, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8034 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 2, 2005
RadiationMonochromator: triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8034 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 24875 / Num. obs: 24875 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.56 Å / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 1PG5

1pg5


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.913 / SU B: 20.13 / SU ML: 0.209 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.44 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27133 1123 5.1 %RANDOM
Rwork0.22257 ---
all0.22501 ---
obs0.22501 20963 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.349 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20.42 Å20 Å2
2--0.85 Å20 Å2
3----1.27 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3494 0 35 77 3606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223582
X-RAY DIFFRACTIONr_angle_refined_deg1.441.9944842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3535437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.28824.467150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.49515676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9581521
X-RAY DIFFRACTIONr_chiral_restr0.0880.2569
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022580
X-RAY DIFFRACTIONr_nbd_refined0.2080.21718
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22447
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2192
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2560.28
X-RAY DIFFRACTIONr_mcbond_it0.6191.52258
X-RAY DIFFRACTIONr_mcangle_it1.08123582
X-RAY DIFFRACTIONr_scbond_it1.41731465
X-RAY DIFFRACTIONr_scangle_it2.214.51260
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 81 -
Rwork0.292 1484 -
obs--97.39 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5788-0.2292-0.3821.37420.32380.8210.0261-0.0836-0.0148-0.07350.0065-0.09920.05590.1775-0.0326-0.06210.0022-0.0073-0.04330.0063-0.099886.093724.289460.1123
21.8742-0.75070.55142.6950.92044.1943-0.0625-0.1976-0.00830.021-0.0316-0.2226-0.0694-0.00260.0941-0.1227-0.0643-0.002-0.02240.0205-0.1259117.567559.863843.1093
36.10811.4138-2.55761.86310.20491.4843-0.0046-0.0263-0.2338-0.0926-0.1155-0.1912-0.03720.06580.1201-0.0576-0.04660.0839-0.04970.0161-0.092101.791242.41747.2624
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 2991 - 300
2X-RAY DIFFRACTION2BB11 - 10015 - 104
3X-RAY DIFFRACTION3BB101 - 160105 - 164

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