4F04 | pdb_00004f04

A Second Allosteric site in E. coli Aspartate Transcarbamoylase: R-state ATCase with UTP bound

PDB DOI: https://doi.org/10.2210/pdb4F04/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-05-03 Released: 2012-07-11
Deposition Author(s): Peterson, A.W., Cockrell, G.M., Kantrowitz, E.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.207 (Depositor), 0.210 (DCC)
R-Value Work:
0.173 (Depositor), 0.179 (DCC)
R-Value Observed:
0.175 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

A second allosteric site in Escherichia coli aspartate transcarbamoylase.

Peterson, A.W., Cockrell, G.M., Kantrowitz, E.R.

(2012) Biochemistry 51: 4776-4778

PubMed: 22667327 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/bi3006219
Primary Citation Related Structures:
4F04

PubMed Abstract:
Escherichia coli aspartate transcarbamoylase is feedback inhibited by CTP and UTP in the presence of CTP. Here, we show by X-ray crystallography that UTP binds to a unique site on each regulatory chain of the enzyme that is near but not overlapping with the known CTP site. These results bring into question all of the previously proposed mechanisms of allosteric regulation in aspartate transcarbamoylase.

Organizational Affiliation

Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, USA.

Macromolecule Content

Total Structure Weight: 104.57 kDa
Atom Count: 7,448
Modeled Residue Count: 906
Deposited Residue Count: 926
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate carbamoyltransferase catalytic chain	A, C	310	Escherichia coli K-12	Mutation(s): 0 Gene Names: b4245, JW4204, 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A786
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate carbamoyltransferase regulatory chain	B, D	153	Escherichia coli K-12	Mutation(s): 0 Gene Names: b4244, JW4203, pyrI EC: 2.1.3.2
UniProt
Find proteins for P0A7F3 (Escherichia coli (strain K12)) Explore P0A7F3 Go to UniProtKB: P0A7F3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7F3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UTP Query on UTP Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain J [auth D] MOL2 format, chain G [auth B] MOL2 format, chain J [auth D] mmCIF format, chain G [auth B] mmCIF format, chain J [auth D]	G [auth B], J [auth D]	URIDINE 5'-TRIPHOSPHATE C₉ H₁₅ N₂ O₁₅ P₃ PGAVKCOVUIYSFO-XVFCMESISA-N		Interactions Focus chain G [auth B] Focus chain J [auth D] Interactions & Density Focus chain G [auth B] Focus chain J [auth D]
PAL Query on PAL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth C] mmCIF format, chain E [auth A] mmCIF format, chain H [auth C]	E [auth A], H [auth C]	N-(PHOSPHONACETYL)-L-ASPARTIC ACID C₆ H₁₀ N O₈ P ZZKNRXZVGOYGJT-VKHMYHEASA-N		Interactions Focus chain E [auth A] Focus chain H [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain I [auth D] MOL2 format, chain F [auth B] MOL2 format, chain I [auth D] mmCIF format, chain F [auth B] mmCIF format, chain I [auth D]	F [auth B], I [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain I [auth D] Interactions & Density Focus chain F [auth B] Focus chain I [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.207 (Depositor), 0.210 (DCC)
R-Value Work: 0.173 (Depositor), 0.179 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.277	α = 90
b = 121.277	β = 90
c = 155.109	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-07-11

Deposition Author(s):

Peterson, A.W.

Cockrell, G.M.

Kantrowitz, E.R.

Revision History (Full details and data files)

Version 1.0: 2012-07-11
Type: Initial release
Version 1.1: 2013-06-26
Changes: Database references
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Derived calculations