5YEI

Mechanistic insight into the regulation of Pseudomonas aeruginosa aspartate kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanistic insights into the allosteric regulation of Pseudomonas aeruginosa aspartate kinase.

Li, C.Yang, M.Liu, L.Li, T.Peng, C.He, L.Song, Y.Zhu, Y.Shen, Y.Yang, J.Zhao, N.Zhao, C.Zhou, Q.Li, H.Kang, M.Tong, A.Tang, H.Bao, R.

(2018) Biochem J 475: 1107-1119

  • DOI: https://doi.org/10.1042/BCJ20170829
  • Primary Citation of Related Structures:  
    5YEI

  • PubMed Abstract: 

    In plants and microorganisms, aspartate kinase (AK) catalyzes an initial commitment step of the aspartate family amino acid biosynthesis. Owing to various structural organizations, AKs from different species show tremendous diversity and complex allosteric controls. We report the crystal structure of AK from Pseudomonas aeruginosa (PaAK), a typical α2β2 hetero-tetrameric enzyme, in complex with inhibitory effectors. Distinctive features of PaAK are revealed by structural and biochemical analyses. Essentially, the open conformation of Lys-/Thr-bound PaAK structure clarifies the inhibitory mechanism of α2β2-type AK. Moreover, the various inhibitory effectors of PaAK have been identified and a general amino acid effector motif of AK family is described.


  • Organizational Affiliation

    Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AspartokinaseA [auth D],
B,
C [auth F],
E [auth H]
164Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: lysCPA0904
EC: 2.7.2.4
UniProt
Find proteins for O69077 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore O69077 
Go to UniProtKB:  O69077
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO69077
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
AspartokinaseD [auth C],
F [auth G],
G [auth A],
H [auth E]
412Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: lysCPA0904
EC: 2.7.2.4
UniProt
Find proteins for O69077 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore O69077 
Go to UniProtKB:  O69077
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO69077
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LYS
Query on LYS

Download Ideal Coordinates CCD File 
N [auth C],
Q [auth G],
S [auth A],
W [auth E]
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
THR
Query on THR

Download Ideal Coordinates CCD File 
I [auth D]
J [auth B]
K [auth F]
L [auth F]
M [auth C]
I [auth D],
J [auth B],
K [auth F],
L [auth F],
M [auth C],
O [auth H],
R [auth G],
T [auth A]
THREONINE
C4 H9 N O3
AYFVYJQAPQTCCC-GBXIJSLDSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
P [auth G],
U [auth E],
V [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.459α = 90
b = 171.793β = 90.29
c = 88.932γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2019-09-11
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description