Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 62.47 kDa 
• Atom Count: 4148 
• Modelled Residue Count: 515 
• Deposited Residue Count: 576 
• Unique protein chains: 1

4DBF

Crystal structures of Cg1458

• PDB DOI: 10.2210/pdb4DBF/pdb

• Classification: ISOMERASE
• Organism(s): Corynebacterium glutamicum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-15 Released: 2012-11-28 
• Deposition Author(s): Ran, T.T., Xu, D.Q., Wang, W.W., Gao, Y.Y., Wang, M.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.244 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Literature

Crystal structures of Cg1458 reveal a catalytic lid domain and a common catalytic mechanism for FAH family.

Ran, T., Gao, Y., Marsh, M., Zhu, W., Wang, M., Mao, X., Xu, L., Xu, D., Wang, W.

(2013) Biochem J 449: 51-60

• PubMed: 23046410 
• DOI: 10.1042/BJ20120913
• Primary Citation of Related Structures:  
  4DBF, 4DBH


• PubMed Abstract: 
  

Cg1458 was recently characterized as a novel soluble oxaloacetate decarboxylase. However, sequence alignment identified that Cg1458 has no similarity with other oxaloacetate decarboxylases and instead belongs to the FAH (fumarylacetoacetate hydrolase) family. Differences in the function of Cg1458 and other FAH proteins may suggest a different catalytic mechanism. To help elucidate the catalytic mechanism of Cg1458, crystal structures of Cg1458 in both the open and closed conformations have been determined for the first time up to a resolution of 1.9 Å (1 Å=0.1 nm) and 2.0 Å respectively. Comparison of both structures and detailed biochemical studies confirmed the presence of a catalytic lid domain which is missing in the native enzyme structure. In this lid domain, a glutamic acid-histidine dyad was found to be critical in mediating enzymatic catalysis. On the basis of structural modelling and comparison, as well as large-scale sequence alignment studies, we further determined that the catalytic mechanism of Cg1458 is actually through a glutamic acid-histidine-water triad, and this catalytic triad is common among FAH family proteins that catalyse the cleavage of the C-C bond of the substrate. Two sequence motifs, HxxE and Hxx…xxE have been identified as the basis for this mechanism.

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Organizational Affiliation: 

Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-HYDROXYHEPTA-2,4-DIENE-1,7-DIOATE ISOMERASE	A, B	288	Corynebacterium glutamicum	Mutation(s): 0  EC: 5.3.3 (PDB Primary Data), 4.1.1 (PDB Primary Data)
UniProt
Find proteins for Q8NQY2 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025)) Explore Q8NQY2  Go to UniProtKB:  Q8NQY2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.244 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.12	α = 90
b = 124.12	β = 90
c = 73.64	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-01-15 
• Released Date: 2012-11-28 
Deposition Author(s): Ran, T.T., Xu, D.Q., Wang, W.W., Gao, Y.Y., Wang, M.T.

Revision History  

• Version 1.0: 2012-11-28
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Data collection, Database references