1R0C | pdb_00001r0c

Products in the T State of Aspartate Transcarbamylase: Crystal Structure of the Phosphate and N-carbamyl-L-aspartate Ligated Enzyme

PDB DOI: https://doi.org/10.2210/pdb1R0C/pdb

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

Deposited: 2003-09-19 Released: 2004-06-08
Deposition Author(s): Huang, J., Lipscomb, W.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free:
0.274 (Depositor)
R-Value Work:
0.226 (Depositor), 0.225 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Products in the T-State of Aspartate Transcarbamylase: Crystal Structure of the Phosphate and N-Carbamyl-l-aspartate Ligated Enzyme

Huang, J., Lipscomb, W.N.

(2004) Biochemistry 43: 6422-6426

PubMed: 15157076 Search on PubMed
DOI: https://doi.org/10.1021/bi0302144
Primary Citation Related Structures:
1R0C

PubMed Abstract:
The structure of aspartate transcarbamylase of Escherichia coli ligated to products (phosphate and N-carbamyl-l-aspartate) has been determined at 2.37 A resolution (R-factor = 0.23, R(free) = 0.27). Results might indicate a product release mode, rather than close analogues to the transition state like those found in our earlier studies of other ligands (N-phosphonacetyl-L-aspartate, carbamyl phosphate plus malonate, phosphonoacetamide plus malonate, or citrate plus phosphate). Ordered product release, first carbamylaspartate (CLA) and then phosphate, might be facilitated by a 4 A movement of phosphate from the substrate-analogue position to the product (phosphate) binding position, and by a somewhat similar release movement of the other product (CLA) relative to its analogue (citrate). This movement is consistent with earlier studies of binding of either pyrophosphate or phosphate alone [Honzatko, R. B., and Lipscomb, W. N. (1982) J. Mol. Biol. 160, 265-286].

Organizational Affiliation

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.

Macromolecule Content

Total Structure Weight: 103.63 kDa
Atom Count: 7,821
Modeled Residue Count: 926
Deposited Residue Count: 926
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate carbamoyltransferase catalytic chain	A, C [auth G]	310	Escherichia coli	Mutation(s): 0 Gene Names: PYRB OR B4245 OR C5345 OR Z5856 OR ECS5222 OR SF4245 OR S4507 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

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate carbamoyltransferase regulatory chain	B, D [auth H]	153	Escherichia coli	Mutation(s): 0 Gene Names: PYRI OR B4244 OR C5344 OR Z5855 OR ECS5221
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
NCD Query on NCD Download:Ideal Coordinates CCD File SDF format, chain I [auth G] SDF format, chain F [auth A] MOL2 format, chain I [auth G] MOL2 format, chain F [auth A] mmCIF format, chain I [auth G] mmCIF format, chain F [auth A]	F [auth A], I [auth G]	N-CARBAMOYL-L-ASPARTATE C₅ H₈ N₂ O₅ HLKXYZVTANABHZ-REOHCLBHSA-N		Interactions Focus chain F [auth A] Focus chain I [auth G] Interactions & Density Focus chain F [auth A] Focus chain I [auth G]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth G] SDF format, chain E [auth A] MOL2 format, chain H [auth G] MOL2 format, chain E [auth A] mmCIF format, chain H [auth G] mmCIF format, chain E [auth A]	E [auth A], H [auth G]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain H [auth G] Interactions & Density Focus chain E [auth A] Focus chain H [auth G]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain J [auth H] SDF format, chain G [auth B] MOL2 format, chain J [auth H] MOL2 format, chain G [auth B] mmCIF format, chain J [auth H] mmCIF format, chain G [auth B]	G [auth B], J [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain J [auth H] Interactions & Density Focus chain G [auth B] Focus chain J [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free: 0.274 (Depositor)
R-Value Work: 0.226 (Depositor), 0.225 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.776	α = 90
b = 128.776	β = 90
c = 198.017	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2004-06-08

Deposition Author(s):

Huang, J.

Lipscomb, W.N.

Revision History (Full details and data files)

Version 1.0: 2004-06-08
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description