4I42

E.coli. 1,4-dihydroxy-2-naphthoyl coenzyme A synthase (ecMenB) in complex with 1-hydroxy-2-naphthoyl-CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.154 

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
1,4-Dihydroxy-2-naphthoyl-CoA synthase
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L
285Escherichia coli K-12Mutation(s): 0 
Gene Names: b2262JW2257menB
EC: 4.1.3.36
Find proteins for P0ABU0 (Escherichia coli (strain K12))
Explore P0ABU0 
Go to UniProtKB:  P0ABU0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1HA
Query on 1HA

Download Ideal Coordinates CCD File 
AA [auth C] , BD [auth L] , EB [auth F] , EC [auth I] , M [auth A] , NB [auth G] , OC [auth J] , T [auth B] , 
AA [auth C],  BD [auth L],  EB [auth F],  EC [auth I],  M [auth A],  NB [auth G],  OC [auth J],  T [auth B],  UA [auth E],  VB [auth H],  WC [auth K]
1-hydroxy-2-naphthoyl-CoA
C32 H42 N7 O18 P3 S
ZHSLHXZSNOSMQG-HSJNEKGZSA-N
 Ligand Interaction
BTB
Query on BTB

Download Ideal Coordinates CCD File 
JA [auth C], LB [auth F], MC [auth I]2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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DA [auth C] , DD [auth L] , GB [auth F] , HB [auth F] , HC [auth I] , OA [auth D] , V [auth B] , XA [auth E] , 
DA [auth C],  DD [auth L],  GB [auth F],  HB [auth F],  HC [auth I],  OA [auth D],  V [auth B],  XA [auth E],  YB [auth H],  YC [auth K]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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BB [auth E] , BC [auth H] , CB [auth E] , CC [auth H] , GD [auth L] , HA [auth C] , IB [auth F] , JC [auth I] , 
BB [auth E],  BC [auth H],  CB [auth E],  CC [auth H],  GD [auth L],  HA [auth C],  IB [auth F],  JC [auth I],  O [auth A],  QA [auth D],  TB [auth G],  X [auth B],  Y [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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BA [auth C] , CA [auth C] , CD [auth L] , FB [auth F] , FC [auth I] , GC [auth I] , KA [auth D] , LA [auth D] , 
BA [auth C],  CA [auth C],  CD [auth L],  FB [auth F],  FC [auth I],  GC [auth I],  KA [auth D],  LA [auth D],  MA [auth D],  NA [auth D],  OB [auth G],  PB [auth G],  PC [auth J],  QC [auth J],  RC [auth J],  U [auth B],  VA [auth E],  WA [auth E],  WB [auth H],  XB [auth H],  XC [auth K]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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AB [auth E] , AC [auth H] , EA [auth C] , ED [auth L] , FA [auth C] , FD [auth L] , GA [auth C] , HD [auth L] , 
AB [auth E],  AC [auth H],  EA [auth C],  ED [auth L],  FA [auth C],  FD [auth L],  GA [auth C],  HD [auth L],  IC [auth I],  N [auth A],  PA [auth D],  QB [auth G],  RB [auth G],  SB [auth G],  W [auth B],  YA [auth E],  ZA [auth E],  ZB [auth H]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

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MB [auth F], NC [auth I], RA [auth D], S [auth A], SA [auth D], TA [auth D], VC [auth J]BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
AD [auth K] , DB [auth E] , DC [auth H] , IA [auth C] , ID [auth L] , JB [auth F] , JD [auth L] , KB [auth F] , 
AD [auth K],  DB [auth E],  DC [auth H],  IA [auth C],  ID [auth L],  JB [auth F],  JD [auth L],  KB [auth F],  KC [auth I],  LC [auth I],  P [auth A],  Q [auth A],  R [auth A],  SC [auth J],  TC [auth J],  UB [auth G],  UC [auth J],  Z [auth B],  ZC [auth K]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.154 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.646α = 90
b = 141.659β = 90
c = 288.477γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
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: 2014-05-07
    Changes: Database references