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- PDB-8atc: COMPLEX OF N-PHOSPHONACETYL-L-ASPARTATE WITH ASPARTATE CARBAMOYLT... -

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Entry
Database: PDB / ID: 8atc
TitleCOMPLEX OF N-PHOSPHONACETYL-L-ASPARTATE WITH ASPARTATE CARBAMOYLTRANSFERASE. X-RAY REFINEMENT, ANALYSIS OF CONFORMATIONAL CHANGES AND CATALYTIC AND ALLOSTERIC MECHANISMS
Components
  • ASPARTATE CARBAMOYLTRANSFERASE (R STATE), 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
N-(PHOSPHONACETYL)-L-ASPARTIC ACID / Aspartate carbamoyltransferase catalytic subunit / Aspartate carbamoyltransferase regulatory chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsKe, H. / Lipscomb, W.N. / Cho, Y. / Honzatko, R.B.
Citation
Journal: J.Mol.Biol. / Year: 1988
Title: Complex of N-phosphonacetyl-L-aspartate with aspartate carbamoyltransferase. X-ray refinement, analysis of conformational changes and catalytic and allosteric mechanisms.
Authors: Ke, H.M. / Lipscomb, W.N. / Cho, Y.J. / Honzatko, R.B.
#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-Angstroms Resolution
Authors: Stevens, R.C. / Gouaux, J.E. / Lipscomb, W.N.
#2: Journal: Biochemistry / Year: 1990
Title: Crystal Structures of Aspartate Carbamoyltransferase Ligated with Phosphonoacetamide, Malonate, and Ctp or ATP at 2.8-Angstroms Resolution and Neutral Ph
Authors: Gouaux, J.E. / Stevens, R.C. / Lipscomb, W.N.
#3: Journal: Biochemistry / Year: 1990
Title: Crystal Structures of Phosphonoacetamide Ligated T and Phosphonoacetamide and Malonate Ligated R States of Aspartate Carbamoyltransferase at 2.8-Angstroms Resolution and Neutral Ph
Authors: Gouaux, J.E. / Lipscomb, W.N.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1989
Title: Structural Transitions in Crystals of Native Aspartate Carbamoyltransferase
Authors: Gouaux, J.E. / Lipscomb, W.N.
#5: Journal: Biochemistry / Year: 1989
Title: Structure of a Single Amino Acid Mutant of Aspartate Carbamoyltransferase at 2.5-Angstroms Resolution. Implications for the Cooperative Mechanism
Authors: Gouaux, J.E. / Lipscomb, W.N. / Middleton, S.A. / Kantrowitz, E.R.
#6: Journal: Science / Year: 1988
Title: Escherichia Coli Aspartate Transcarbamylase. The Relation between Structure and Function
Authors: Kantrowitz, E.R. / Lipscomb, W.N.
#7: Journal: Proc.Natl.Acad.Sci.USA / Year: 1988
Title: Three-Dimensional Structure of Carbamoyl Phosphate and Succinate Bound to Aspartate Carbamoyltransferase
Authors: Gouaux, J.E. / Lipscomb, W.N.
#8: Journal: J.Mol.Biol. / Year: 1987
Title: Structural Asymmetry in the Ctp-Liganded Form of Aspartate Carbamoyltransferase from Escherichia Coli
Authors: Kim, K.H. / Pan, Z. / Honzatko, R.B. / Ke, H. / Lipscomb, W.N.
#9: Journal: J.Mol.Biol. / Year: 1987
Title: 2.5 Angstroms Structure of Aspartate Carbamoyltransferase Complexed with the Bisubstrate Analog N-(Phosphonacetyl)-L-Aspartate
Authors: Krause, K.L. / Volz, K.W. / Lipscomb, W.N.
#10: Journal: Biochem.Biophys.Res.Commun. / Year: 1987
Title: The Catalytic Mechanism of Escherichia Coli Aspartate Carbamoyltransferase. A Molecular Modelling Study
Authors: Gouaux, J.E. / Krause, K.L. / Lipscomb, W.N.
#11: Journal: Proc.Natl.Acad.Sci.USA / Year: 1985
Title: Structure at 2.9-Angstroms Resolution of Aspartate Carbamoyltransferase Complexed with the Bisubstrate Analogue N-(Phosphonacetyl)-L-Aspartate
Authors: Krause, K.L. / Volz, K.W. / Lipscomb, W.N.
#12: Journal: Proc.Natl.Acad.Sci.USA / Year: 1984
Title: Structure of Unligated Aspartate Carbamoyltransferase of Escherichia Coli at 2.6-Angstroms Resolution
Authors: Ke, H. / Honzatko, R.B. / Lipscomb, W.N.
#13: 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. / Edwards, B.F.P. / Evans, D.R. / Warren, S.G. / Wiley, D.C. / Ladner, R.C. / Lipscomb, W.N.
#14: 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.
#15: 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.
#16: 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.
#17: 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.
#18: Journal: Proc.Natl.Acad.Sci.USA / Year: 1978
Title: Three-Dimensional Structures of Aspartate Carbamoyltransferase from Escherichia Coli and of its Complex with Cytidine Triphosphate
Authors: Monaco, H.L. / Crawford, J.L. / Lipscomb, W.N.
#19: 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.
#20: 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
DepositionAug 25, 1989Processing site: BNL
Revision 1.0Oct 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ASPARTATE CARBAMOYLTRANSFERASE (R STATE), CATALYTIC CHAIN
B: ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
C: ASPARTATE CARBAMOYLTRANSFERASE (R STATE), CATALYTIC CHAIN
D: ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4608
Polymers102,8194
Non-polymers6414
Water16,790932
1
A: ASPARTATE CARBAMOYLTRANSFERASE (R STATE), CATALYTIC CHAIN
B: ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
C: ASPARTATE CARBAMOYLTRANSFERASE (R STATE), CATALYTIC CHAIN
D: ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
hetero molecules

A: ASPARTATE CARBAMOYLTRANSFERASE (R STATE), CATALYTIC CHAIN
B: ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
C: ASPARTATE CARBAMOYLTRANSFERASE (R STATE), CATALYTIC CHAIN
D: ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
hetero molecules

A: ASPARTATE CARBAMOYLTRANSFERASE (R STATE), CATALYTIC CHAIN
B: ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
C: ASPARTATE CARBAMOYLTRANSFERASE (R STATE), CATALYTIC CHAIN
D: ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)310,38124
Polymers308,45812
Non-polymers1,92312
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 area31700 Å2
ΔGint-108.2 kcal/mol
Surface area103800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.110, 122.110, 156.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Atom site foot note1: RESIDUES PRO A 268 AND PRO C 268 ARE CIS-PROLINES.

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Components

#1: Protein ASPARTATE CARBAMOYLTRANSFERASE (R STATE), CATALYTIC CHAIN


Mass: 34337.105 Da / Num. of mol.: 2
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: 17072.549 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0A7F3
#3: Chemical ChemComp-PAL / N-(PHOSPHONACETYL)-L-ASPARTIC ACID


Mass: 255.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10NO8P
#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 / Water


Mass: 18.015 Da / Num. of mol.: 932 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.36 %
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: dialyze
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-18 mg/mlprotein solution11
250 mMmaleic acid12
350 mMN-ethylmorpholine12
41 mMPALA12
53 mM12NaN3

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→15 Å
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / Num. obs: 51500 / % possible obs: 84.7 % / Rmerge F obs: 2 / Num. measured all: 415000

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.5→8 Å / Rfactor obs: 0.165
Details: THERE IS A NON-CRYSTALLOGRAPHIC TWO-FOLD AXIS WHICH RELATES THE *A* AND *B* CHAINS TO THE *C* AND *D* CHAINS.
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7106 0 34 932 8072
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d00.014
X-RAY DIFFRACTIONp_angle_d00.037
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d00.055
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.51.599
X-RAY DIFFRACTIONp_mcangle_it2.82.815
X-RAY DIFFRACTIONp_scbond_it2.32.396
X-RAY DIFFRACTIONp_scangle_it44.085
X-RAY DIFFRACTIONp_plane_restr00.011
X-RAY DIFFRACTIONp_chiral_restr0.10.149
X-RAY DIFFRACTIONp_singtor_nbd0.20.206
X-RAY DIFFRACTIONp_multtor_nbd0.20.243
X-RAY DIFFRACTIONp_xhyhbond_nbd0.20.224
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor22.1
X-RAY DIFFRACTIONp_staggered_tor1717.7
X-RAY DIFFRACTIONp_orthonormal_tor3131.1
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.5 Å / Num. reflection obs: 40697 / Rfactor obs: 0.165
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0370.03
X-RAY DIFFRACTIONp_planar_d0.0550.06
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.1490.15
X-RAY DIFFRACTIONp_mcbond_it1.5991.5
X-RAY DIFFRACTIONp_scbond_it2.3962
X-RAY DIFFRACTIONp_mcangle_it2.8152
X-RAY DIFFRACTIONp_scangle_it4.0853

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