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- PDB-8bpl: Aspartate transcarbamoylase mutant (N2045C, R2238C) from Chaetomi... -

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Basic information

Entry
Database: PDB / ID: 8bpl
TitleAspartate transcarbamoylase mutant (N2045C, R2238C) from Chaetomium thermophilum CAD-like bound to carbamoyl phosphate
ComponentsCarbamoyl-phosphate synthase (glutamine-hydrolyzing)
KeywordsTRANSFERASE / Nucleotide metabolism / de novo pyrimidine synthesis / CAD / cysteine / disulfide bridge / protein stability / crosslinking / succinate / multienzymatic protein
Function / homology
Function and homology information


carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / aspartate carbamoyltransferase activity / amino acid binding / glutamine metabolic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / hydrolase activity / ATP binding / metal ion binding
Similarity search - Function
Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthase large subunit, CPSase domain / Carbamoyl-phosphate synthase, small subunit / Carbamoyl-phosphate synthase, large subunit / Carbamoyl-phosphate synthase small subunit, GATase1 domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain superfamily / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily / Carbamoyl-phosphate synthase small chain, CPSase domain / Carbamoyl-phosphate synthetase large chain, oligomerisation domain ...Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthase large subunit, CPSase domain / Carbamoyl-phosphate synthase, small subunit / Carbamoyl-phosphate synthase, large subunit / Carbamoyl-phosphate synthase small subunit, GATase1 domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain superfamily / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily / Carbamoyl-phosphate synthase small chain, CPSase domain / Carbamoyl-phosphate synthetase large chain, oligomerisation domain / Carbamoyl-phosphate synthetase large chain, oligomerisation domain / Carbamoyl-phosphate synthase small chain, CPSase domain / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain profile. / MGS-like domain / Aspartate carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Glutamine amidotransferase / Aspartate/ornithine carbamoyltransferase superfamily / Glutamine amidotransferase class-I / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Glutamine amidotransferase type 1 domain profile. / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / Class I glutamine amidotransferase-like / Metal-dependent hydrolase / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / SUCCINIC ACID / Uncharacterized protein
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
Authorsdel Cano-Ochoa, F. / Ramon-Maiques, S.
Funding support Spain, 2items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)RTI2018-098084-B-I00 Spain
Ministerio de Ciencia e Innovacion (MCIN)PID2021-128468NB-I00 Spain
CitationJournal: Molecules / Year: 2023
Title: A Tailored Strategy to Crosslink the Aspartate Transcarbamoylase Domain of the Multienzymatic Protein CAD.
Authors: Del Cano-Ochoa, F. / Rubio-Del-Campo, A. / Ramon-Maiques, S.
History
DepositionNov 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbamoyl-phosphate synthase (glutamine-hydrolyzing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3949
Polymers35,5821
Non-polymers8128
Water5,152286
1
A: Carbamoyl-phosphate synthase (glutamine-hydrolyzing)
hetero molecules

A: Carbamoyl-phosphate synthase (glutamine-hydrolyzing)
hetero molecules

A: Carbamoyl-phosphate synthase (glutamine-hydrolyzing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,18127
Polymers106,7463
Non-polymers2,43524
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area13300 Å2
ΔGint-50 kcal/mol
Surface area34110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.410, 139.410, 139.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332
Space group name HallP4acd2ab3
Symmetry operation#1: x,y,z
#2: x+3/4,-z+3/4,y+1/4
#3: x+1/4,z+3/4,-y+3/4
#4: z+1/4,y+3/4,-x+3/4
#5: -z+3/4,y+1/4,x+3/4
#6: -y+3/4,x+1/4,z+3/4
#7: y+3/4,-x+3/4,z+1/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+1/4,x+3/4,-z+3/4
#20: -y+1/4,-x+1/4,-z+1/4
#21: z+3/4,-y+3/4,x+1/4
#22: -z+1/4,-y+1/4,-x+1/4
#23: -x+3/4,z+1/4,y+3/4
#24: -x+1/4,-z+1/4,-y+1/4
Components on special symmetry positions
IDModelComponents
11A-2404-

GOL

21A-2719-

HOH

31A-2734-

HOH

41A-2739-

HOH

51A-2760-

HOH

61A-2777-

HOH

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Components

#1: Protein Carbamoyl-phosphate synthase (glutamine-hydrolyzing)


Mass: 35582.113 Da / Num. of mol.: 1 / Mutation: N2045C, R2238C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Gene: CTHT_0032600 / Plasmid: pOPIN-M-ctATC2Cys / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0S583
#2: Chemical ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER


Mass: 141.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4NO5P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.23 Å3/Da / Density % sol: 61.89 % / Description: Bipyramidal-shaped crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.8 M succinic acid pH 7.0 cocrystallized with carbamoyl phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.58→49.29 Å / Num. obs: 900158 / % possible obs: 99.7 % / Redundancy: 14.2 % / Biso Wilson estimate: 25.37 Å2 / CC1/2: 1 / Net I/σ(I): 19.8
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 1.1 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 78877 / CC1/2: 0.45 / % possible all: 96.8

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Processing

Software
NameVersionClassification
EDNA1.20.1_4487data collection
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NNQ

5nnq


Resolution: 1.58→49.29 Å / SU ML: 0.1736 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.0271
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1706 3142 4.97 %
Rwork0.1357 60050 -
obs0.1375 63192 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.76 Å2
Refinement stepCycle: LAST / Resolution: 1.58→49.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 0 52 286 2816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01282657
X-RAY DIFFRACTIONf_angle_d1.33463611
X-RAY DIFFRACTIONf_chiral_restr0.07414
X-RAY DIFFRACTIONf_plane_restr0.0189466
X-RAY DIFFRACTIONf_dihedral_angle_d8.7179389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.60.31311140.23662299X-RAY DIFFRACTION85.08
1.6-1.630.27471360.21492709X-RAY DIFFRACTION99.96
1.63-1.660.2451330.1962718X-RAY DIFFRACTION99.96
1.66-1.690.24561380.18312673X-RAY DIFFRACTION100
1.69-1.720.2281720.17642698X-RAY DIFFRACTION100
1.72-1.760.32111450.21532700X-RAY DIFFRACTION100
1.76-1.790.29971440.1912693X-RAY DIFFRACTION100
1.8-1.840.25061350.1582750X-RAY DIFFRACTION100
1.84-1.880.18291230.12012711X-RAY DIFFRACTION100
1.88-1.930.1671380.10852731X-RAY DIFFRACTION100
1.93-1.990.17451320.10822733X-RAY DIFFRACTION100
1.99-2.050.15531480.10342709X-RAY DIFFRACTION100
2.06-2.130.14771220.10872735X-RAY DIFFRACTION100
2.13-2.210.17671260.11182771X-RAY DIFFRACTION100
2.21-2.310.14171470.09932733X-RAY DIFFRACTION100
2.31-2.440.1491690.10462730X-RAY DIFFRACTION100
2.44-2.590.13241370.11432763X-RAY DIFFRACTION99.97
2.59-2.790.15341660.12422758X-RAY DIFFRACTION100
2.79-3.070.1781530.13322761X-RAY DIFFRACTION100
3.07-3.510.17061360.13152817X-RAY DIFFRACTION100
3.51-4.430.14151660.12582838X-RAY DIFFRACTION100
4.43-100.18231620.1763020X-RAY DIFFRACTION99.56

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