4GO5 | pdb_00004go5

The regulatory subunit of aspartate kinase from Mycobacterium tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb4GO5/pdb

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


• Deposited: 2012-08-18 Released: 2012-09-05 
• Deposition Author(s): Yang, Q., Li, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.252 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

Structural view of the regulatory subunit of aspartate kinase from Mycobacterium tuberculosis.

Yang, Q., Yu, K., Yan, L., Li, Y., Chen, C., Li, X.

(2011) Protein Cell 2: 745-754

• PubMed: 21976064 
• DOI: https://doi.org/10.1007/s13238-011-1094-2
• Primary Citation Related Structures: 
  4GO5, 4GO7


• PubMed Abstract: 
  

  The aspartate kinase (AK) from Mycobacterium tuberculosis (Mtb) catalyzes the biosynthesis of aspartate family amino acids, including lysine, threonine, isoleucine and methionine. We determined the crystal structures of the regulatory subunit of aspartate kinase from Mtb alone (referred to as MtbAKβ) and in complex with threonine (referred to as MtbAKβ-Thr) at resolutions of 2.6 Å and 2.0 Å, respectively. MtbAKβ is composed of two perpendicular non-equivalent ACT domains [aspartate kinase, chorismate mutase, and TyrA (prephenate dehydrogenase)] per monomer. Each ACT domain contains two α helices and four antiparallel β strands. The structure of MtbAKβ shares high similarity with the regulatory subunit of the aspartate kinase from Corynebacterium glutamicum (referred to as CgAKβ), suggesting similar regulatory mechanisms. Biochemical assays in our study showed that MtbAK is inhibited by threonine. Based on crystal structure analysis, we discuss the regulatory mechanism of MtbAK.

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Organizational Affiliation: 
• National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

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)

Macromolecule Content 

• Total Structure Weight: 21.5 kDa 
• Atom Count: 1,261 
• Modeled Residue Count: 167 
• Deposited Residue Count: 200 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartokinase	A [auth X]	200	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: ask, Rv3709c, MT3812, MTV025.057c EC: 2.7.2.4
UniProt
Find proteins for P9WPX3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPX3  Go to UniProtKB:  P9WPX3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.252 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.791	α = 90
b = 64.791	β = 90
c = 136.981	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-05 
Deposition Author(s): Yang, Q., Li, X.

Revision History  

• Version 1.0: 2012-09-05
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references