3FLM

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.270
R-Value Work: 0.182
R-Value Observed: 0.186

wwPDB Validation 3D Report Full Report

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

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 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2009.01.168
Primary Citation of 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P17109
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.270
R-Value Work: 0.182
R-Value Observed: 0.186
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-03-24

Deposition Author(s):

Priyadarshi, A.

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.