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- PDB-2fzg: The Structure of Wild-Type E. Coli Aspartate Transcarbamoylase in... -

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Basic information

Entry
Database: PDB / ID: 2fzg
TitleThe Structure of Wild-Type E. Coli Aspartate Transcarbamoylase in Complex with Novel T State Inhibitors at 2.25 Resolution
Components(Aspartate carbamoyltransferase ...) x 2
KeywordsTRANSFERASE / Inhibitors / allosteric transition / Xray structures
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
CYTIDINE-5'-TRIPHOSPHATE / Chem-EOB / Aspartate carbamoyltransferase catalytic subunit / Aspartate carbamoyltransferase regulatory chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsHeng, S. / Stieglitz, K.A. / Eldo, J. / Xia, J. / Cardia, J.P. / Kantrowitz, E.R.
CitationJournal: Biochemistry / Year: 2006
Title: T-state Inhibitors of E. coli Aspartate Transcarbamoylase that Prevent the Allosteric Transition.
Authors: Heng, S. / Stieglitz, K.A. / Eldo, J. / Xia, J. / Cardia, J.P. / Kantrowitz, E.R.
History
DepositionFeb 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _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_asym_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_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 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)104,76310
Polymers102,9614
Non-polymers1,8016
Water9,746541
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)314,28930
Polymers308,88412
Non-polymers5,40418
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 area39990 Å2
ΔGint-75 kcal/mol
Surface area99890 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)119.940, 119.940, 141.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

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Aspartate carbamoyltransferase ... , 2 types, 4 molecules ACBD

#1: Protein Aspartate carbamoyltransferase catalytic chain / Aspartate transcarbamylase / ATCase


Mass: 34337.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PYRB / Plasmid: PEK54 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A786, aspartate carbamoyltransferase
#2: Protein Aspartate carbamoyltransferase 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) / Gene: PYRI / Plasmid: PEK54 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A7F3, aspartate carbamoyltransferase

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Non-polymers , 4 types, 547 molecules

#3: Chemical ChemComp-EOB / {1,3-PHENYLENEBIS[IMINO(2-OXOETHANE-2,1-DIYL)]}BIS(PHOSPHONIC ACID) / 2,2'-(1,3-PHENYLENEBIS(AZANEDIYL))BIS(2-OXOETHANE-2,1DIYL)DIPHOSPHONIC ACID


Mass: 352.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N2O8P2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 541 / 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: 2.86 Å3/Da / Density % sol: 57.02 %
Crystal growTemperature: 298 K / Method: microdialysis / pH: 5.7
Details: ATCase holoenzyme was crystallized by microdialysis, using 50 L wells. The enzyme solution, at ~18 mg/mL, was dialyzed against a solution of 40 mM citric acid, 3 mM sodium azide, 1 mM 2- ...Details: ATCase holoenzyme was crystallized by microdialysis, using 50 L wells. The enzyme solution, at ~18 mg/mL, was dialyzed against a solution of 40 mM citric acid, 3 mM sodium azide, 1 mM 2-mercaptoethanol, 1 mM cytidine 5 -triphosphate, 0.2 mM EDTA (pH 5.7), MICRODIALYSIS, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→28.23 Å / Num. all: 79872 / Num. obs: 79872 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.62 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.24 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 3.9 / Num. unique all: 7836 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
d*TREKdata reduction
AMoREphasing
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ZA2

1za2


Resolution: 2.25→28.23 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 5744 -Random
Rwork0.201 ---
all0.201 56470 --
obs0.201 56307 99.7 %-
Refinement stepCycle: LAST / Resolution: 2.25→28.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7216 0 104 541 7861

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