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- PDB-2atc: CRYSTAL AND MOLECULAR STRUCTURES OF NATIVE AND CTP-LIGANDED ASPAR... -

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Entry
Database: PDB / ID: 2atc
TitleCRYSTAL AND MOLECULAR STRUCTURES OF NATIVE AND CTP-LIGANDED ASPARTATE CARBAMOYLTRANSFERASE FROM ESCHERICHIA COLI
Components
  • ASPARTATE CARBAMOYLTRANSFERASE, CATALYTIC CHAIN
  • ASPARTATE CARBAMOYLTRANSFERASE, REGULATORY CHAIN
KeywordsTRANSFERASE (CARBAMOYL-P / ASPARTATE)
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 / cytosol / cytoplasm
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
Aspartate carbamoyltransferase catalytic subunit / Aspartate carbamoyltransferase regulatory chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsHonzatko, R.B. / Crawford, J.L. / Monaco, H.L. / Ladner, J.E. / Edwards, B.F.P. / Evans, D.R. / Warren, S.G. / Wiley, D.C. / Ladner, R.C. / Lipscomb, W.N.
Citation
Journal: J.Mol.Biol. / Year: 1982
Title: Crystal and molecular structures of native and CTP-liganded aspartate carbamoyltransferase from Escherichia coli.
Authors: Honzatko, R.B. / Crawford, J.L. / Monaco, H.L. / Ladner, J.E. / Ewards, B.F. / Evans, D.R. / Warren, S.G. / Wiley, D.C. / Ladner, R.C. / Lipscomb, W.N.
#1: Journal: Science / Year: 1988
Title: Escherichia Coli Aspartate Transcarbamylase. The Relation between Structure and Function
Authors: Kantrowitz, E.R. / Lipscomb, W.N.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1982
Title: Interactions of Metal-Nucleotide Complexes with Aspartate Carbamoyltransferase in the Crystalline State
Authors: Honzatko, R.B. / Lipscomb, W.N.
#3: Journal: J.Mol.Biol. / Year: 1982
Title: Interactions of Phosphate Ligands with Escherichia Coli Aspartate Carbamoyltransferase in the Crystalline State
Authors: Honzatko, R.B. / Lipscomb, W.N.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1982
Title: Gross Quaternary Changes in Aspartate Carbamoyltransferase are Induced by the Binding of N-(Phosphonacetyl)-L-Aspartate. A 3.5-Angstroms Resolution Study
Authors: Ladner, J.E. / Kitchell, J.P. / Honzatko, R.B. / Ke, H.M. / Volz, K.W. / Kalb(Gilboa), A.J. / Ladner, R.C. / Lipscomb, W.N.
#5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1979
Title: A 3.0-Angstroms Resolution Study of Nucleotide Complexes with Aspartate Carbamoyltransferase
Authors: Honzatko, R.B. / Monaco, H.L. / Lipscomb, W.N.
#6: Journal: Proc.Natl.Acad.Sci.USA / Year: 1978
Title: Three-Dimensional Structures of Aspartate Carbamoyltransferase from Escherichia Coli and of its Complex with Cytidine Triposphate
Authors: Monaco, H.L. / Crawford, J.L. / Lipscomb, W.N.
#7: Journal: STRUCTURE AND CONFORMATION OF NUCLEIC ACIDS AND PROTEIN-NUCLEIC ACID INTERACTIONS : PROCEEDINGS OF THE FOURTH ANNUAL HARRY STEENBOCK SYMPOSIUM, JUNE 16-19, 1974, MADISON, WISCONSIN
Year: 1975
Title: Binding Site at 5.5 Angstroms Resolution of Cytidine Triphosphate, the Allosteric Inhibitor of Aspartate Transcarbamylase from Escherichia Coli. Relation to Mechanisms of Control
Authors: Lipscomb, W.N. / Edwards, B.F.P. / Evans, D.R. / Pastra-Landis, S.C.
#8: Journal: Proc.Natl.Acad.Sci.USA / Year: 1973
Title: Aspartate Transcarbamoylase from Escherichia Coli. Electron Density at 5.5 Angstroms Resolution
Authors: Warren, S.G. / Edwards, B.F.P. / Evans, D.R. / Wiley, D.C. / Lipscomb, W.N.
History
DepositionMar 24, 1982Processing site: BNL
Revision 1.0Dec 7, 1982Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ASPARTATE CARBAMOYLTRANSFERASE, CATALYTIC CHAIN
B: ASPARTATE CARBAMOYLTRANSFERASE, REGULATORY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6353
Polymers50,5702
Non-polymers651
Water00
1
A: ASPARTATE CARBAMOYLTRANSFERASE, CATALYTIC CHAIN
B: ASPARTATE CARBAMOYLTRANSFERASE, REGULATORY CHAIN
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)303,81018
Polymers303,41812
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area30140 Å2
ΔGint-138 kcal/mol
Surface area122010 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)131.700, 131.700, 199.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Atom site foot note1: THESE ATOMS ARE NOT CLEARLY DEFINED IN THE FOURIER MAPS.
2: THE SIDE CHAINS OF THESE RESIDUES WERE NOT LOCATED IN THE FOURIER MAPS.

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Components

#1: Protein ASPARTATE CARBAMOYLTRANSFERASE, CATALYTIC CHAIN


Mass: 33551.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0A786, aspartate carbamoyltransferase
#2: Protein ASPARTATE CARBAMOYLTRANSFERASE, REGULATORY CHAIN


Mass: 17018.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0A7F3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.48 %
Crystal grow
*PLUS
Method: microdialysis / pH: 6.35
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1buttom
20.05 MTris-HCl1reservior
30.05 Mimidazole1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 3 Å / Num. obs: 10764 / Num. measured all: 47214

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor Rwork: 0.27 / Highest resolution: 3 Å
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3510 0 1 0 3511
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.032
X-RAY DIFFRACTIONo_angle_d0.083
X-RAY DIFFRACTIONo_planar_d0.118
X-RAY DIFFRACTIONo_plane_restr0.024
X-RAY DIFFRACTIONo_chiral_restr0.315

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