4P69

Acek (D477A) ICDH complex

• PDB DOI: https://doi.org/10.2210/pdb4P69/pdb

• Classification: TRANSFERASE, HYDROLASE/OXIDOREDUCTASE
• Organism(s): Escherichia coli O157:H7, Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-03-22 Released: 2014-10-08 
• Deposition Author(s): Jimin, Z., Nan, W., Shu, W., Zongchao, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.247 
• R-Value Work: 0.177 
• R-Value Observed: 0.180 

Literature

The phosphatase mechanism of bifunctional kinase/phosphatase AceK.

Wang, S., Shen, Q., Chen, G., Zheng, J., Tan, H., Jia, Z.

(2014) Chem Commun (Camb) 50: 14117-14120

• PubMed: 25272278 
• DOI: https://doi.org/10.1039/c4cc05375c
• Primary Citation of Related Structures:  
  4P69


• PubMed Abstract: 
  

  We have revealed that bifunctional AceK kinase/phosphatase utilizes a stepwise addition-elimination mechanism in its dephosphorylation reaction. This work explains how AceK enables opposite kinase and phosphatase activities with Asp477 and a single Mg(2+) ion.

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Organizational Affiliation: 

College of Chemistry, Beijing Normal University, Beijing, 100875, China. [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 225.9 kDa 
• Atom Count: 15,755 
• Modelled Residue Count: 1,945 
• Deposited Residue Count: 1,966 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate dehydrogenase kinase/phosphatase	A, B	568	Escherichia coli O157:H7	Mutation(s): 1  Gene Names: aceK, Z5602, ECs4934 EC: 2.7.11.5 (PDB Primary Data), 3.1.3 (PDB Primary Data)
UniProt
Find proteins for Q8X607 (Escherichia coli O157:H7) Explore Q8X607  Go to UniProtKB:  Q8X607

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate dehydrogenase [NADP]	C, D	415	Escherichia coli K-12	Mutation(s): 0  Gene Names: icd, icdA, icdE, b1136, JW1122 EC: 1.1.1.42
UniProt
Find proteins for P08200 (Escherichia coli (strain K12)) Explore P08200  Go to UniProtKB:  P08200

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	F [auth A], G [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
AMP	E [auth A], H [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.247 
• R-Value Work: 0.177 
• R-Value Observed: 0.180 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 198.16	α = 90
b = 198.16	β = 90
c = 156.071	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-08 
Deposition Author(s): Jimin, Z., Nan, W., Shu, W., Zongchao, J.

Revision History  

• Version 1.0: 2014-10-08
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
• Version 1.2: 2018-05-16
  Changes: Data collection, Database references
• Version 1.3: 2018-05-30
  Changes: Advisory, Data collection, Derived calculations, Source and taxonomy
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Refinement description