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- PDB-1ezz: CRYSTAL STRUCTURE OF E. COLI ASPARTATE TRANSCARBAMOYLASE P268A MU... -

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Basic information

Entry
Database: PDB / ID: 1ezz
TitleCRYSTAL STRUCTURE OF E. COLI ASPARTATE TRANSCARBAMOYLASE P268A MUTANT IN THE T-STATE
Components
  • ASPARTATE CARBAMOYLTRANSFERASE CATALYTIC CHAIN
  • ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
KeywordsTRANSFERASE / aspartate transcarbamoylase / aspartate carbamoyltransferase / cis-proline / cis-amino acid
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
Aspartate carbamoyltransferase catalytic subunit / Aspartate carbamoyltransferase regulatory chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsJin, L. / Stec, B. / Kantrowitz, E.R.
Citation
Journal: Biochemistry / Year: 2000
Title: A cis-proline to alanine mutant of E. coli aspartate transcarbamoylase: kinetic studies and three-dimensional crystal structures.
Authors: Jin, L. / 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.
History
DepositionMay 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: 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 / _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 1.4Feb 7, 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 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)103,0406
Polymers102,9094
Non-polymers1312
Water4,450247
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)309,12118
Polymers308,72812
Non-polymers3926
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)129.870, 129.870, 198.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-338-

HOH

DetailsThe biological assembly is a dodecamer. The entire molecule requires two symmetry partners generated by rotations around the three-fold

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Components

#1: Protein ASPARTATE CARBAMOYLTRANSFERASE CATALYTIC CHAIN / ASPARTATE TRANSCARBAMOYLASE CATALYTIC CHAIN


Mass: 34311.070 Da / Num. of mol.: 2 / Mutation: P268A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Plasmid: PEK412, A PLASMID WITH THE PYRBI GENES INSERTED INTO PUC119
Production host: Escherichia coli (E. coli) / References: UniProt: P0A786, aspartate carbamoyltransferase
#2: Protein ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN / ASPARTATE TRANSCARBAMOYLASE REGULATORY CHAIN


Mass: 17143.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Plasmid: PEK412, A PLASMID WITH THE PYRBI GENES INSERTED INTO PUC119
Production host: Escherichia coli (E. coli) / References: UniProt: P0A7F3
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 247 / 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: 3.13 Å3/Da / Density % sol: 60.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ENZYME: 24 mg/ml; 1:1 enzyme to-buffer ratio, BUFFER: 20 mm HEPES, 14% (w/v) PEG 1450, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
124 mg/mlenzyme1drop
214 %(w/v)PEG14501reservoir
320 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: UCSD MARK III / Detector: AREA DETECTOR / Date: Jun 19, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 34450 / Num. obs: 34422 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 4.296
Reflection shellResolution: 2.7→2.91 Å / Redundancy: 2.17 % / Rmerge(I) obs: 0.427 / Num. unique all: 13768 / % possible all: 99.8

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
SDMSdata reduction
SDMSdata scaling
RefinementResolution: 2.7→8 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2900 -random
Rwork0.182 ---
all-32931 --
obs-29421 89.3 %-
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7228 0 2 247 7477
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.86
X-RAY DIFFRACTIONx_dihedral_angle_d25.6
X-RAY DIFFRACTIONx_improper_angle_d1.57
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.57

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