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- PDB-1m6v: Crystal Structure of the G359F (small subunit) Point Mutant of Ca... -

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Basic information

Entry
Database: PDB / ID: 1m6v
TitleCrystal Structure of the G359F (small subunit) Point Mutant of Carbamoyl Phosphate Synthetase
Components
  • carbamoyl phosphate synthetase large chain
  • carbamoyl-phosphate synthetase small chain
KeywordsLIGASE / substrate channeling / tunnel
Function / homology
Function and homology information


carbamoyl-phosphate synthase complex / : / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / pyrimidine nucleobase biosynthetic process / glutaminase activity / L-arginine biosynthetic process / glutamine metabolic process ...carbamoyl-phosphate synthase complex / : / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / pyrimidine nucleobase biosynthetic process / glutaminase activity / L-arginine biosynthetic process / glutamine metabolic process / amino acid binding / amino acid biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / protein heterodimerization activity / nucleotide binding / ATP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthase large chain, methylglyoxal synthase-like domain / Carbamoyl Phosphate Synthetase; Chain A, domain 4 / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / : / Methylglyoxal synthase-like 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 small subunit, N-terminal domain / Carbamoyl-phosphate synthase large chain, methylglyoxal synthase-like domain / Carbamoyl Phosphate Synthetase; Chain A, domain 4 / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / : / Methylglyoxal synthase-like 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 / Glucose Oxidase; domain 1 / Rossmann fold - #20 / Glutamine amidotransferase / Glutamine amidotransferase class-I / Carbamoyl-phosphate synthase subdomain signature 1. / Glutamine amidotransferase type 1 domain profile. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / ATP-grasp fold, A domain / Class I glutamine amidotransferase (GATase) domain / Pre-ATP-grasp domain superfamily / ATP-grasp fold, B domain / ATP-grasp fold / ATP-grasp fold profile. / Class I glutamine amidotransferase-like / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / 3-Layer(bba) Sandwich / Carbamoyl-phosphate synthase subdomain signature 2. / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / : / TETRAETHYLAMMONIUM ION / L-ornithine / PHOSPHATE ION / Carbamoyl-phosphate synthase small chain / Carbamoyl phosphate synthase large chain / Carbamoyl phosphate synthase small chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsThoden, J.B. / Huang, X. / Raushel, F.M. / Holden, H.M.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Carbamoyl-phosphate synthetase. Creation of an escape route for ammonia
Authors: Thoden, J.B. / Huang, X. / Raushel, F.M. / Holden, H.M.
History
DepositionJul 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 20, 2019Group: Advisory / Derived calculations
Category: database_PDB_caveat / pdbx_struct_conn_angle ...database_PDB_caveat / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE THE CLONE USED VARIED FROM THE SWISS-PROT ENTRY AT RESIDUE 46 OF CHAINS ACEG (SWS P00968) ...SEQUENCE THE CLONE USED VARIED FROM THE SWISS-PROT ENTRY AT RESIDUE 46 OF CHAINS ACEG (SWS P00968) AND RESIDUE 183 OF CHAINS BDFH (SWS P00907).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: carbamoyl phosphate synthetase large chain
B: carbamoyl-phosphate synthetase small chain
C: carbamoyl phosphate synthetase large chain
D: carbamoyl-phosphate synthetase small chain
E: carbamoyl phosphate synthetase large chain
F: carbamoyl-phosphate synthetase small chain
G: carbamoyl phosphate synthetase large chain
H: carbamoyl-phosphate synthetase small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)645,73094
Polymers638,2158
Non-polymers7,51686
Water64,1513561
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.500, 164.200, 331.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBiological assembly is an (ab)4 hetero-tetramer: Comprised of chains A,B,C,D,E,F,G,H

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
carbamoyl phosphate synthetase large chain / Carbamoyl-phosphate synthetase ammonia chain


Mass: 117982.688 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CARB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3)pLysS
References: UniProt: P00968, carbamoyl-phosphate synthase (glutamine-hydrolysing)
#2: Protein
carbamoyl-phosphate synthetase small chain / Carbamoyl-phosphate synthetase glutamine chain


Mass: 41571.016 Da / Num. of mol.: 4 / Mutation: G359F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CARA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3)pLysS
References: UniProt: P00907, UniProt: P0A6F1*PLUS, carbamoyl-phosphate synthase (glutamine-hydrolysing)

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Non-polymers , 8 types, 3647 molecules

#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn
#4: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: K
#5: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#7: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#8: Chemical
ChemComp-ORN / L-ornithine


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12N2O2
#9: Chemical
ChemComp-NET / TETRAETHYLAMMONIUM ION


Mass: 130.251 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H20N
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3561 / 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: 3.23 Å3/Da / Density % sol: 61.91 %
Crystal growTemperature: 277 K / Method: batch / pH: 7.4
Details: PEG-8000, manganese chloride, potassium chloride, ADP, ornithine, tetraethylammonium chloride, HEPPS, pH 7.4, batch, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
18 %PEG800011
20.65 MTEA11
30.5 mM11MnCl2
4100 mM11KCl
51.5 mMADP11
60.5 mML-ormithine11
725 mMHEPPS11pH7.4

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.70004 Å
DetectorType: SBC-2 / Detector: CCD / Date: Dec 11, 1999
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.70004 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 445772 / Num. obs: 445772 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.0706 / Net I/σ(I): 16.2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 40543 / Rsym value: 0.244 / % possible all: 84.4
Reflection
*PLUS
Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 84.4 % / Num. unique obs: 40543 / Rmerge(I) obs: 0.244

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Processing

Software
NameClassification
d*TREKdata scaling
HKL-2000data reduction
TNTrefinement
d*TREKdata reduction
HKL-2000data scaling
TNTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1JDB

1jdb


Resolution: 2.1→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 44271 -random
Rwork0.174 ---
all0.18 440901 --
obs0.18 440901 92.4 %-
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44124 0 374 3561 48059
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg2.33
Refinement
*PLUS
Highest resolution: 2.1 Å / Num. reflection obs: 396875 / Num. reflection Rfree: 44026 / Rfactor all: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_planar_d0.006
X-RAY DIFFRACTIONt_plane_restr0.012

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