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: 2.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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:  
    4I42, 4I4Z, 4I52

  • 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 Escherichia coli and Synechocystis sp ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Naphthoate synthase
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I
275Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Gene Names: menBsll1127
EC: 4.1.3.36
Find proteins for P73495 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Explore P73495 
Go to UniProtKB:  P73495
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2NE
Query on 2NE

Download Ideal Coordinates CCD File 
AA [auth I] , J [auth A] , L [auth B] , N [auth C] , Q [auth D] , S [auth E] , U [auth F] , W [auth G] , 
AA [auth I],  J [auth A],  L [auth B],  N [auth C],  Q [auth D],  S [auth E],  U [auth F],  W [auth G],  Y [auth H]
Salicylyl CoA
C28 H40 N7 O18 P3 S
YTKKDFTVSNSVEE-TYHXJLICSA-N
 Ligand Interaction
MLI
Query on MLI

Download Ideal Coordinates CCD File 
CA [auth I], P [auth C]MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
BCT
Query on BCT

Download Ideal Coordinates CCD File 
BA [auth I] , K [auth A] , M [auth B] , O [auth C] , R [auth D] , T [auth E] , V [auth F] , X [auth G] , 
BA [auth I],  K [auth A],  M [auth B],  O [auth C],  R [auth D],  T [auth E],  V [auth F],  X [auth G],  Z [auth H]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.21α = 90
b = 139.21β = 90
c = 220.981γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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