4MYD

1.37 Angstrom Crystal Structure of E. Coli 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (MenH) in complex with SHCHC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.130 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Molecular basis of the general base catalysis of an alpha / beta-hydrolase catalytic triad.

Sun, Y.Yin, S.Feng, Y.Li, J.Zhou, J.Liu, C.Zhu, G.Guo, Z.

(2014) J Biol Chem 289: 15867-15879

  • DOI: 10.1074/jbc.M113.535641
  • Primary Citation of Related Structures:  
    4MXD, 4MYD, 4MYS

  • PubMed Abstract: 
  • The serine-histidine-aspartate triad is well known for its covalent, nucleophilic catalysis in a diverse array of enzymatic transformations. Here we show that its nucleophilicity is shielded and its catalytic role is limited to being a specific general base by an open-closed conformational change in the catalysis of (1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (or MenH), a typical α/β-hydrolase fold enzyme in the vitamin K biosynthetic pathway ...

    The serine-histidine-aspartate triad is well known for its covalent, nucleophilic catalysis in a diverse array of enzymatic transformations. Here we show that its nucleophilicity is shielded and its catalytic role is limited to being a specific general base by an open-closed conformational change in the catalysis of (1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (or MenH), a typical α/β-hydrolase fold enzyme in the vitamin K biosynthetic pathway. This enzyme is found to adopt an open conformation without a functional triad in its ligand-free form and a closed conformation with a fully functional catalytic triad in the presence of its reaction product. The open-to-closed conformational transition involves movement of half of the α-helical cap domain, which causes extensive structural changes in the α/β-domain and forces the side chain of the triad histidine to adopt an energetically disfavored gauche conformation to form the functional triad. NMR analysis shows that the inactive open conformation without a triad prevails in ligand-free solution and is converted to the closed conformation with a properly formed triad by the reaction product. Mutation of the residues crucial to this open-closed transition either greatly decreases or completely eliminates the enzyme activity, supporting an important catalytic role for the structural change. These findings suggest that the open-closed conformational change tightly couples formation of the catalytic triad to substrate binding to enhance the substrate specificities and simultaneously shield the nucleophilicity of the triad, thus allowing it to expand its catalytic power beyond the nucleophilic catalysis.


    Organizational Affiliation

    From the Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region (SAR), China and chguo@ust.hk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthaseA, B, C252Escherichia coli K-12Mutation(s): 0 
Gene Names: b2263JW2258menHyfbB
EC: 4.2.99.20
UniProt
Find proteins for P37355 (Escherichia coli (strain K12))
Explore P37355 
Go to UniProtKB:  P37355
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37355
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
164
Query on 164

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B]
2-(3-CARBOXYPROPIONYL)-6-HYDROXY-CYCLOHEXA-2,4-DIENE CARBOXYLIC ACID
C11 H12 O6
QJYRAJSESKVEAE-PSASIEDQSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
164 Binding MOAD:  4MYD Kd: 2.80e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.130 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.85α = 90
b = 121.85β = 90
c = 46.85γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-23
    Type: Initial release
  • Version 1.1: 2014-05-07
    Changes: Database references
  • Version 1.2: 2022-08-24
    Changes: Database references, Derived calculations