2H3E

Structure of wild-type E. coli Aspartate Transcarbamoylase in the presence of N-phosphonacetyl-L-isoasparagine at 2.3A resolution

PDB DOI: https://doi.org/10.2210/pdb2H3E/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2006-05-22 Released: 2006-10-17
Deposition Author(s): Eldo, J., Cardia, J.P., O'Day, E.M., Xia, J., Tsuruta, H., Kantrowitz, E.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.250
R-Value Work: 0.206
R-Value Observed: 0.206

Starting Model: experimental
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This is version 1.4 of the entry. See complete history.

Literature

N-Phosphonacetyl-l-isoasparagine a Potent and Specific Inhibitor of Escherichia coli Aspartate Transcarbamoylase.

Eldo, J., Cardia, J.P., O'day, E.M., Xia, J., Tsuruta, H., Kantrowitz, E.R.

(2006) J Med Chem 49: 5932-5938

PubMed: 17004708 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/jm0607294
Primary Citation of Related Structures:
2H3E

PubMed Abstract:
The synthesis of a new inhibitor, N-phosphonacetyl-L-isoasparagine (PALI), of Escherichia coli aspartate transcarbamoylase (ATCase) is reported, as well as structural studies of the enzyme.PALI complex. PALI was synthesized in 7 steps from beta-benzyl L-aspartate. The KD of PALI was 2 microM. Kinetics and small-angle X-ray scattering experiments showed that PALI can induce the cooperative transition of ATCase from the T to the R state. The X-ray structure of the enzyme.PALI complex showed 22 hydrogen-bonding interactions between the enzyme and PALI. The kinetic characterization and crystal structure of the ATCase.PALI complex also provides detailed information regarding the importance of the alpha-carboxylate for the binding of the substrate aspartate.

Organizational Affiliation

Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachussetts 02467-3808, USA.

Macromolecule Content

Total Structure Weight: 103.6 kDa
Atom Count: 7,609
Modelled Residue Count: 910
Deposited Residue Count: 926
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate carbamoyltransferase catalytic chain	A, C	310	Escherichia coli	Mutation(s): 0 Gene Names: pyrB EC: 2.1.3.2
UniProt
Find proteins for P0A786 (Escherichia coli (strain K12)) Explore P0A786 Go to UniProtKB: P0A786
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A786
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate carbamoyltransferase regulatory chain	B, D	153	Escherichia coli	Mutation(s): 0 Gene Names: pyrI
UniProt
Find proteins for P0A7F3 (Escherichia coli (strain K12)) Explore P0A7F3 Go to UniProtKB: P0A7F3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A7F3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6PR Query on 6PR Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth C] mmCIF format, chain E [auth A] mmCIF format, chain G [auth C]	E [auth A], G [auth C]	(S)-4-AMINO-4-OXO-3-(2-PHOSPHONOACETAMIDO)BUTANOIC ACID C₆ H₁₁ N₂ O₇ P HCFYWDYKLQITSR-VKHMYHEASA-N		Interactions Focus chain E [auth A] Focus chain G [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain H [auth D] MOL2 format, chain F [auth B] MOL2 format, chain H [auth D] mmCIF format, chain F [auth B] mmCIF format, chain H [auth D]	F [auth B], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain H [auth D] Interactions & Density Focus chain F [auth B] Focus chain H [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
6PR	PDBBind: 2H3E	Kd: 2000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.250
R-Value Work: 0.206
R-Value Observed: 0.206
Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.32	α = 90
b = 120.32	β = 90
c = 154.51	γ = 120

Software Package:

Software Name	Purpose
d*TREK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-10-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-10-17
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description