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- PDB-1a9x: CARBAMOYL PHOSPHATE SYNTHETASE: CAUGHT IN THE ACT OF GLUTAMINE HY... -

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Basic information

Entry
Database: PDB / ID: 1a9x
TitleCARBAMOYL PHOSPHATE SYNTHETASE: CAUGHT IN THE ACT OF GLUTAMINE HYDROLYSIS
Components(CARBAMOYL PHOSPHATE SYNTHETASE ...) x 2
KeywordsAMIDOTRANSFERASE / THIOESTER
Function / homology
Function and homology information


carbamoyl-phosphate synthase complex / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / pyrimidine nucleobase biosynthetic process / arginine biosynthetic process / glutaminase activity / : / amino acid binding ...carbamoyl-phosphate synthase complex / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / pyrimidine nucleobase biosynthetic process / arginine biosynthetic process / glutaminase activity / : / amino acid binding / glutamine metabolic process / 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 / cytosol / cytoplasm
Similarity search - Function
Carbamoyl Phosphate Synthetase; Chain A, domain 4 / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthase large chain, methylglyoxal synthase-like 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 Synthetase; Chain A, domain 4 / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthase large chain, methylglyoxal synthase-like 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 / MGS-like domain profile. / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain / Glutamine amidotransferase class-I / Glutamine amidotransferase / Rossmann fold - #20 / Glucose Oxidase; domain 1 / 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 / ATP-grasp fold, B domain / Pre-ATP-grasp domain superfamily / 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsThoden, J. / Holden, H.
CitationJournal: Biochemistry / Year: 1998
Title: Carbamoyl phosphate synthetase: caught in the act of glutamine hydrolysis.
Authors: Thoden, J.B. / Miran, S.G. / Phillips, J.C. / Howard, A.J. / Raushel, F.M. / Holden, H.M.
History
DepositionApr 14, 1998Processing site: BNL
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Dec 21, 2022Group: 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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
Revision 1.5Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)645,640111
Polymers636,8458
Non-polymers8,795103
Water81,5724528
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CARBAMOYL PHOSPHATE SYNTHETASE (LARGE CHAIN)
B: CARBAMOYL PHOSPHATE SYNTHETASE (SMALL CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,43428
Polymers159,2112
Non-polymers2,22226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-77 kcal/mol
Surface area46650 Å2
MethodPISA, PQS
3
G: CARBAMOYL PHOSPHATE SYNTHETASE (LARGE CHAIN)
H: CARBAMOYL PHOSPHATE SYNTHETASE (SMALL CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,43428
Polymers159,2112
Non-polymers2,22226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8710 Å2
ΔGint-76 kcal/mol
Surface area46880 Å2
MethodPISA, PQS
4
C: CARBAMOYL PHOSPHATE SYNTHETASE (LARGE CHAIN)
D: CARBAMOYL PHOSPHATE SYNTHETASE (SMALL CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,43428
Polymers159,2112
Non-polymers2,22226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8740 Å2
ΔGint-74 kcal/mol
Surface area46920 Å2
MethodPISA, PQS
5
E: CARBAMOYL PHOSPHATE SYNTHETASE (LARGE CHAIN)
F: CARBAMOYL PHOSPHATE SYNTHETASE (SMALL CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,33927
Polymers159,2112
Non-polymers2,12725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint-72 kcal/mol
Surface area46700 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)152.100, 164.400, 332.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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CARBAMOYL PHOSPHATE SYNTHETASE ... , 2 types, 8 molecules ACEGBDFH

#1: Protein
CARBAMOYL PHOSPHATE SYNTHETASE (LARGE CHAIN)


Mass: 117956.656 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P00968
#2: Protein
CARBAMOYL PHOSPHATE SYNTHETASE (SMALL CHAIN)


Mass: 41254.520 Da / Num. of mol.: 4 / Mutation: H353N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P00907, UniProt: P0A6F1*PLUS

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Non-polymers , 8 types, 4631 molecules

#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


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


Mass: 39.098 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: K
#6: Chemical...
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine 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 / 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 / Tetraethylammonium


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


Mass: 18.015 Da / Num. of mol.: 4528 / 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: 3.25 Å3/Da / Density % sol: 62 %
Crystal growpH: 7.4
Details: 0.65M NET4CL 8% PEG 8000 100MM KCL 2.5MM MNCL2 2.5MM ADP 2.5MM ORNITHINE 5MM GLUTAMINE 25MM HEPES PH 7.4 THEN SOAKED INTO: 1.4M NET4CL 8% PEG 8000 250MM KCL 2.5MM MNCL2 2.5MM ADP 2.5MM ...Details: 0.65M NET4CL 8% PEG 8000 100MM KCL 2.5MM MNCL2 2.5MM ADP 2.5MM ORNITHINE 5MM GLUTAMINE 25MM HEPES PH 7.4 THEN SOAKED INTO: 1.4M NET4CL 8% PEG 8000 250MM KCL 2.5MM MNCL2 2.5MM ADP 2.5MM ORNITHINE 5MM GLUTAMINE 25MM HEPES PH 7.4 7.5% ETHYLENE GLYCOL
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 277 K / pH: 8 / Method: batch method / Details: Thoden, J.B., (1995) Acta Crysta., D51, 827.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mM11KCl
20.5 mML-ornithine11
30.5 mM11MnCl2
42.5 mMADP11
58 %PEG800011
60.65 Mtetraethylammonium chloride11
712.5 mMHEPPS11
82.5 mM11BeF3
95 mMglutamine11

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.2
DetectorType: BRUKER / Detector: CCD / Date: Nov 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 700998 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 23.8
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 2 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 4 / Rsym value: 0.275 / % possible all: 91
Reflection
*PLUS
Num. measured all: 1676492
Reflection shell
*PLUS
% possible obs: 91 % / Num. unique obs: 85888 / Num. measured obs: 170785

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
SAINT2000data reduction
XCALIBREdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JDB

1jdb


Resolution: 1.8→30 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
all0.191 700998 -
obs-700998 92 %
Solvent computationSolvent model: TNT / Bsol: 290.8 Å2 / ksol: 0.99 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44248 0 435 4528 49211
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.014454676
X-RAY DIFFRACTIONt_angle_deg2.526130710
X-RAY DIFFRACTIONt_dihedral_angle_d17.7274210
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.008122918
X-RAY DIFFRACTIONt_gen_planes0.01657950
X-RAY DIFFRACTIONt_it0493100
X-RAY DIFFRACTIONt_nbd0.032367
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.70
X-RAY DIFFRACTIONt_planar_d0.00818
X-RAY DIFFRACTIONt_plane_restr0.0150

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