3FLM | pdb_00003flm

Crystal structure of menD from E.coli

• PDB DOI: https://doi.org/10.2210/pdb3FLM/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-12-19 Released: 2009-03-24 
• Deposition Author(s): Priyadarshi, A., Hwang, K.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.270 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Structural insights of the MenD from Escherichia coli reveal ThDP affinity.

Priyadarshi, A., Saleem, Y., Nam, K.H., Kim, K.S., Park, S.Y., Kim, E.E., Hwang, K.Y.

(2009) Biochem Biophys Res Commun 380: 797-801

• PubMed: 19338755 
• DOI: https://doi.org/10.1016/j.bbrc.2009.01.168
• Primary Citation Related Structures: 
  3FLM


• PubMed Abstract: 
  

  MenD (2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate) synthase belongs to the superfamily of thiamin diphosphate-dependent decarboxylases, which converts isochorismate and 2-oxoglutarate to SHCHC, pyruvate, and carbon dioxide. Here, we report the first crystal structure of apo-MenD from Escherichia coli determined in tetragonal crystal form. The subunit displays the typical three-domain structure observed for ThDP-dependent enzymes. Analytical gel filtration shows that EcMenD behaves as a dimer as well as a tetramer. Circular dichroism and isothermal calorimetry results confirm EcMenD dependency on ThDP, which concomitantly helps to stabilize with better configuration.

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Organizational Affiliation: 
• Biomedical Research Center, Life Science Division, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 136-791, Republic of Korea.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 122.9 kDa 
• Atom Count: 8,317 
• Modeled Residue Count: 1,066 
• Deposited Residue Count: 1,112 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase	A, B	556	Escherichia coli K-12	Mutation(s): 1  Gene Names: b2264, JW5374, menD EC: 2.2.1.9
UniProt
Find proteins for P17109 (Escherichia coli (strain K12)) Explore P17109  Go to UniProtKB:  P17109

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.270 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.067	α = 90
b = 118.067	β = 90
c = 176.477	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-24 
Deposition Author(s): Priyadarshi, A., Hwang, K.Y.

Revision History  

• Version 1.0: 2009-03-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-04-18
  Changes: Database references
• Version 1.3: 2021-11-10
  Changes: Database references
• Version 1.4: 2023-11-01
  Changes: Data collection, Refinement description