4P69 | pdb_00004p69

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free:
0.247 (Depositor), 0.270 (DCC)
R-Value Work:
0.177 (Depositor), 0.221 (DCC)
R-Value Observed:
0.180 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1039/c4cc05375c
Primary Citation 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.

Organizational Affiliation

College of Chemistry, Beijing Normal University, Beijing, 100875, China. jimin_z@bnu.edu.cn hongwei.tan@bnu.edu.cn.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8X607
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08200
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A]	F [auth A], G [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth B]
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.247 (Depositor), 0.270 (DCC)
R-Value Work: 0.177 (Depositor), 0.221 (DCC)
R-Value Observed: 0.180 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-10-08

Deposition Author(s):

Revision History (Full details and data files)

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