7MQV | pdb_00007mqv

Crystal structure of truncated (ACT domain removed) prephenate dehydrogenase tyrA from Bacillus anthracis in complex with NAD

• PDB DOI: https://doi.org/10.2210/pdb7MQV/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus anthracis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-05-06 Released: 2021-05-19 
• Deposition Author(s): Shabalin, I.G., Gritsunov, A., Gabryelska, A., Czub, M.P., Grabowski, M., Cooper, D.R., Christendat, D., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of Bacillus anthracis prephenate dehydrogenase identified an ACT regulatory domain and a novel mode of metabolic regulation for proteins within the prephenate dehydrogenase family of enzyme

Shabalin, I.G., Hou, J., Christendat, D., Minor, W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 140.78 kDa 
• Atom Count: 9,564 
• Modeled Residue Count: 1,160 
• Deposited Residue Count: 1,236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prephenate dehydrogenase	A, B, C, D	309	Bacillus anthracis	Mutation(s): 0  Gene Names: tyrA, GBAA_2954 EC: 1.3.1.12
UniProt
Find proteins for Q81P63 (Bacillus anthracis) Explore Q81P63  Go to UniProtKB:  Q81P63

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
GOL	I [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	J [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.774	α = 90
b = 118.882	β = 92.39
c = 75.558	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-05-19 
Deposition Author(s): Shabalin, I.G., Gritsunov, A., Gabryelska, A., Czub, M.P., Grabowski, M., Cooper, D.R., Christendat, D., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C

Revision History  

• Version 1.0: 2021-05-19
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description