4DBF

Crystal structures of Cg1458

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 

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This is version 1.1 of the entry. See complete history. 


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

  • 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 ...

    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.

    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
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2-HYDROXYHEPTA-2,4-DIENE-1,7-DIOATE ISOMERASEA, B288Corynebacterium glutamicumMutation(s): 0 
EC: 5.3.3 (PDB Primary Data), 4.1.1 (PDB Primary Data)
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download Ideal Coordinates CCD File 
 C [auth A], D [auth A], E [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
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 = 124.12α = 90
b = 124.12β = 90
c = 73.64γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

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