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- PDB-1nbe: ASPARTATE TRANSCARBAMOYLASE REGULATORY CHAIN MUTANT (T82A) -

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Basic information

Entry
Database: PDB / ID: 1nbe
TitleASPARTATE TRANSCARBAMOYLASE REGULATORY CHAIN MUTANT (T82A)
Components(ASPARTATE TRANSCARBAMOYLASE) x 2
KeywordsTRANSFERASE / ATCASE / ALLOSTERY / PYRIMIDINE BIOSYNTHESIS
Function / homology
Function and homology information


aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid binding / glutamine metabolic process / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding ...aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid binding / glutamine metabolic process / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding / identical protein binding / cytoplasm / cytosol
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
D-MALATE / Aspartate carbamoyltransferase catalytic subunit / Aspartate carbamoyltransferase regulatory chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / RIGID BODY / Resolution: 2.6 Å
AuthorsWilliams, M.K. / Stec, B. / Kantrowitz, E.R.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: A single mutation in the regulatory chain of Escherichia coli aspartate transcarbamoylase results in an extreme T-state structure.
Authors: Williams, M.K. / Stec, B. / Kantrowitz, E.R.
#1: Journal: Biochemistry / Year: 1990
Title: Structural Consequences of Effector Binding to the T State of Aspartate Carbamoyltransferase: Crystal Structures of the Unligated and ATP-and Ctp-Complexed Enzymes at 2.6-A Resolution
Authors: Stevens, R.C. / Gouaux, J.E. / Lipscomb, W.N.
#2: Journal: Biochemistry / Year: 1990
Title: Erratum. Structural Consequences of Effector Binding to the T State of Aspartate Carbamoyltransferase: Crystal Structures of the Unligated and ATP-and Ctp-Complexed Enzymes at 2.6-A Resolution
Authors: Stevens, R.C. / Gouaux, J.E. / Lipscomb, W.N.
History
DepositionApr 25, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_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
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ASPARTATE TRANSCARBAMOYLASE
B: ASPARTATE TRANSCARBAMOYLASE
C: ASPARTATE TRANSCARBAMOYLASE
D: ASPARTATE TRANSCARBAMOYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,56910
Polymers102,9014
Non-polymers6676
Water9,908550
1
A: ASPARTATE TRANSCARBAMOYLASE
B: ASPARTATE TRANSCARBAMOYLASE
C: ASPARTATE TRANSCARBAMOYLASE
D: ASPARTATE TRANSCARBAMOYLASE
hetero molecules

A: ASPARTATE TRANSCARBAMOYLASE
B: ASPARTATE TRANSCARBAMOYLASE
C: ASPARTATE TRANSCARBAMOYLASE
D: ASPARTATE TRANSCARBAMOYLASE
hetero molecules

A: ASPARTATE TRANSCARBAMOYLASE
B: ASPARTATE TRANSCARBAMOYLASE
C: ASPARTATE TRANSCARBAMOYLASE
D: ASPARTATE TRANSCARBAMOYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)310,70630
Polymers308,70412
Non-polymers2,00118
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
Buried area33540 Å2
ΔGint-86 kcal/mol
Surface area107580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)122.470, 122.470, 142.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-334-

HOH

21A-335-

HOH

31A-413-

HOH

41A-435-

HOH

51C-442-

HOH

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Components

#1: Protein ASPARTATE TRANSCARBAMOYLASE


Mass: 34337.105 Da / Num. of mol.: 2 / Mutation: T82A
Source method: isolated from a genetically manipulated source
Details: ENZYME INHIBITED WITH MALIC ACID / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PURBI / Plasmid: PEK233 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A786, aspartate carbamoyltransferase
#2: Protein ASPARTATE TRANSCARBAMOYLASE


Mass: 17113.600 Da / Num. of mol.: 2 / Mutation: T82A
Source method: isolated from a genetically manipulated source
Details: ENZYME INHIBITED WITH MALIC ACID / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PURBI / Plasmid: PEK233 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A7F3, aspartate carbamoyltransferase
#3: Chemical
ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 3.3 Å3/Da / Density % sol: 59.03 %
Crystal growpH: 5.85
Details: 7.5 MG/ML PROTEIN DIALYZED AGAINST 100MM MALIC ACID AT PH 5.85,
Crystal grow
*PLUS
pH: 5.8 / Method: microdialysis
Details: Ke, H.M., (1984) Proc.Natl.Acad.Sci.U.S.A., 81, 4037.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-10 mg/mlprotein11
2100 mMmaleic acid12
310 mMTris-HCl12
41 mM2-mercaptoethanol12
50.2 mMEDTA12
60.3 mM12NaN3

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Data collection

DiffractionMean temperature: 292 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jul 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→31.2 Å / Num. obs: 38085 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 6.3
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 1.2 / % possible all: 88.5
Reflection
*PLUS
Num. all: 39763 / Num. obs: 37782

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
SDMSdata reduction
SDMSdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: RIGID BODY
Starting model: 6AT1

6at1


Resolution: 2.6→10 Å / Isotropic thermal model: ALL ATOMS / Cross valid method: IMPLOR-CYCLING TEST SETS / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.237 3631 10 %
Rwork0.177 --
obs0.177 36315 85 %
Displacement parametersBiso mean: 22.31 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7228 0 38 550 7816
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.95
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.73
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.5
X-RAY DIFFRACTIONx_mcangle_it3.5
X-RAY DIFFRACTIONx_scbond_it3.5
X-RAY DIFFRACTIONx_scangle_it3.5
LS refinement shellResolution: 2.6→2.72 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.297 4 10 %
Rwork0.24 3698 -
obs--85 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.73
LS refinement shell
*PLUS
Rfactor Rwork: 0.24

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