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- PDB-1acm: ARGININE 54 IN THE ACTIVE SITE OF ESCHERICHIA COLI ASPARTATE TRAN... -

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Database: PDB / ID: 1acm
TitleARGININE 54 IN THE ACTIVE SITE OF ESCHERICHIA COLI ASPARTATE TRANSCARBAMOYLASE IS CRITICAL FOR CATALYSIS: A SITE-SPECIFIC MUTAGENESIS, NMR AND X-RAY CRYSTALLOGRAPHY STUDY
Components
  • ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
  • ASPARTATE CARBAMOYLTRANSFERASE, CATALYTIC CHAIN
KeywordsTRANSFERASE (CARBAMOYL-P / ASPARTATE)
Function / homology
Function and homology information


aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / glutamine metabolic process / amino acid binding / 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 / glutamine metabolic process / amino acid binding / 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 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 carbamoyltransferase / Aspartate/ornithine 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
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsStevens, R.C. / Kantrowitz, E.R. / Lipscomb, W.N.
Citation
Journal: Protein Sci. / Year: 1992
Title: Arginine 54 in the active site of Escherichia coli aspartate transcarbamoylase is critical for catalysis: a site-specific mutagenesis, NMR, and X-ray crystallographic study.
Authors: Stebbins, J.W. / Robertson, D.E. / Roberts, M.F. / Stevens, R.C. / Lipscomb, W.N. / 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-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
DepositionJul 8, 1992Processing site: BNL
Revision 1.0Jul 15, 1992Provider: 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 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)103,2888
Polymers102,6474
Non-polymers6414
Water27015
1
A: ASPARTATE CARBAMOYLTRANSFERASE, CATALYTIC CHAIN
B: ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
C: ASPARTATE CARBAMOYLTRANSFERASE, CATALYTIC CHAIN
D: ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
hetero molecules

A: ASPARTATE CARBAMOYLTRANSFERASE, CATALYTIC CHAIN
B: ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
C: ASPARTATE CARBAMOYLTRANSFERASE, CATALYTIC CHAIN
D: ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
hetero molecules

A: ASPARTATE CARBAMOYLTRANSFERASE, CATALYTIC CHAIN
B: ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
C: ASPARTATE CARBAMOYLTRANSFERASE, CATALYTIC CHAIN
D: ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,86424
Polymers307,94112
Non-polymers1,92312
Water1086
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 area31610 Å2
ΔGint-137 kcal/mol
Surface area99550 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)122.200, 122.200, 156.200
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.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.105647, -0.993868, 0.03264), (-0.994085, 0.104725, -0.02877), (0.025176, -0.035486, -0.999053)
Vector: 101.9998, 92.8371, 80.1865)
DetailsTHE NON-CRYSTALLOGRAPHIC TWO-FOLD AXIS, WHICH IS SPECIFIED ON THE *MTRIX* RECORDS BELOW, RELATES THE *A* AND *B* CHAINS TO THE *C* AND *D* CHAINS.

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Components

#1: Protein ASPARTATE CARBAMOYLTRANSFERASE, CATALYTIC CHAIN


Mass: 34250.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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
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


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Compound detailsACTIVE BINDING CATALYTIC CHAIN (CHAINS A AND C) RESIDUE ARGININE 54 IN THE ACTIVE BINDING SITE HAS ...ACTIVE BINDING CATALYTIC CHAIN (CHAINS A AND C) RESIDUE ARGININE 54 IN THE ACTIVE BINDING SITE HAS BEEN REPLACED WITH ALANINE BY SITE-SPECIFIC MUTAGENESIS.

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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
Temperature: 21 ℃ / pH: 5.9 / Method: microdialysis / Details: Krause, K.L., (1987) J.Mol.Biol., 193, 527.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-16 mg/mlenzyme1buttom
250 mMmaleic acid1reservior
31 mMN-(phosphonacetyl)-L-aspartate1reservoir
43 mM1reservoirNaN3
5N-ethylmorpholine1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. all: 33922 / Num. obs: 33351 / Redundancy: 6.9 %

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.8→8 Å / Rfactor Rwork: 0.18
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7094 0 34 15 7143
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg3.1
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 8 Å / Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg

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