4I4Z

Synechocystis sp. PCC 6803 1,4-dihydroxy-2-naphthoyl-coenzyme A synthase (MenB) in complex with salicylyl-CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of the induced-fit mechanism of 1,4-dihydroxy-2-naphthoyl coenzyme a synthase from the crotonase fold superfamily

Sun, Y.Song, H.Li, J.Li, Y.Jiang, M.Zhou, J.Guo, Z.

(2013) Plos One 8: e63095-e63095

  • DOI: 10.1371/journal.pone.0063095
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 1, 4-Dihydroxy-2-naphthoyl coenzyme A (DHNA-CoA) synthase is a typical crotonase fold enzyme with an implicated role of conformational changes in catalysis. We have identified these conformational changes by determining the structures of its Escheric ...

    1, 4-Dihydroxy-2-naphthoyl coenzyme A (DHNA-CoA) synthase is a typical crotonase fold enzyme with an implicated role of conformational changes in catalysis. We have identified these conformational changes by determining the structures of its Escherichia coli and Synechocystis sp. PCC6803 orthologues in complex with a product analog. The structural changes include the folding of an active-site loop into a β-hairpin and significant reorientation of a helix at the carboxy terminus. Interestingly, a new interface is formed between the ordered loop and the reoriented helix, both of which also form additional interactions with the coenzyme A moiety of the ligand. Site-directed mutation of the amino acid residues involved in these ligand-induced interactions significantly diminishes the enzyme activity. These results suggest a catalytically essential induced-fit that is likely initiated by the enzyme-ligand interactions at the active site.


    Organizational Affiliation

    Department of Chemistry and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Naphthoate synthase
A, B, C, D, E, F, G, H, I
275Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: menB
EC: 4.1.3.36
Find proteins for P73495 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  P73495
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLI
Query on MLI

Download SDF File 
Download CCD File 
C, I
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
BCT
Query on BCT

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
2NE
Query on 2NE

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I
Salicylyl CoA
C28 H40 N7 O18 P3 S
YTKKDFTVSNSVEE-TYHXJLICSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.198 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 139.210α = 90.00
b = 139.210β = 90.00
c = 220.981γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-08
    Type: Initial release
  • Version 1.1: 2013-06-19
    Type: Database references