1QB4 | pdb_00001qb4

CRYSTAL STRUCTURE OF MN(2+)-BOUND PHOSPHOENOLPYRUVATE CARBOXYLASE

• PDB DOI: https://doi.org/10.2210/pdb1QB4/pdb

• Classification: LYASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-04-30 Released: 2002-05-01 
• Deposition Author(s): Matsumura, H., Terada, M., Shirakata, S., Inoue, T., Yoshinaga, T., Izui, K., Kai, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.261 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

Plausible phosphoenolpyruvate binding site revealed by 2.6 A structure of Mn2+-bound phosphoenolpyruvate carboxylase from Escherichia coli

Matsumura, H., Terada, M., Shirakata, S., Inoue, T., Yoshinaga, T., Izui, K., Kai, Y.

(1999) FEBS Lett 458: 93-96

• PubMed: 10481043 
• DOI: https://doi.org/10.1016/s0014-5793(99)01103-5
• Primary Citation Related Structures: 
  1QB4


• PubMed Abstract: 
  

  We have determined the crystal structure of Mn2+-bound Escherichia coli phosphoenolpyruvate carboxylase (PEPC) using X-ray diffraction at 2.6 A resolution, and specified the location of enzyme-bound Mn2+, which is essential for catalytic activity. The electron density map reveals that Mn2+ is bound to the side chain oxygens of Glu-506 and Asp-543, and located at the top of the alpha/beta barrel in PEPC. The coordination sphere of Mn2+ observed in E. coli PEPC is similar to that of Mn2+ found in the pyruvate kinase structure. The model study of Mn2+-bound PEPC complexed with phosphoenolpyruvate (PEP) reveals that the side chains of Arg-396, Arg-581 and Arg-713 could interact with PEP.

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Organizational Affiliation: 
• Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Japan.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 99.36 kDa 
• Atom Count: 6,926 
• Modeled Residue Count: 874 
• Deposited Residue Count: 883 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOENOLPYRUVATE CARBOXYLASE	A	883	Escherichia coli	Mutation(s): 0  Gene Names: K12 EC: 4.1.1.31
UniProt
Find proteins for P00864 (Escherichia coli (strain K12)) Explore P00864  Go to UniProtKB:  P00864

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ASP	C [auth A]	ASPARTIC ACID C4 H7 N O4 CKLJMWTZIZZHCS-REOHCLBHSA-N
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.261 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.75	α = 90
b = 248.41	β = 90
c = 83.47	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-05-01 
Deposition Author(s): Matsumura, H., Terada, M., Shirakata, S., Inoue, T., Yoshinaga, T., Izui, K., Kai, Y.

Revision History  

• Version 1.0: 2002-05-01
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-05-23
  Changes: Data collection, Derived calculations
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations