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

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.154 

Starting Model: experimental
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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


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: https://doi.org/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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
1,4-Dihydroxy-2-naphthoyl-CoA synthase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
285Escherichia coli K-12Mutation(s): 0 
Gene Names: b2262JW2257menB
Find proteins for P0ABU0 (Escherichia coli (strain K12))
Explore P0ABU0 
Go to UniProtKB:  P0ABU0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABU0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 1HA

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AA [auth C]
BD [auth L]
EB [auth F]
EC [auth I]
M [auth A]
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]
C32 H42 N7 O18 P3 S
Query on BTB

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JA [auth C],
LB [auth F],
MC [auth I]
C8 H19 N O5
Query on PEG

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DA [auth C]
DD [auth L]
GB [auth F]
HB [auth F]
HC [auth I]
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]
C4 H10 O3
Query on SO4

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BB [auth E]
BC [auth H]
CB [auth E]
CC [auth H]
GD [auth L]
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]
O4 S
Query on GOL

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BA [auth C]
CA [auth C]
CD [auth L]
FB [auth F]
FC [auth I]
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]
C3 H8 O3
Query on EDO

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AB [auth E]
AC [auth H]
EA [auth C]
ED [auth L]
FA [auth C]
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]
C2 H6 O2
Query on BCT

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MB [auth F]
NC [auth I]
RA [auth D]
S [auth A]
SA [auth D]
MB [auth F],
NC [auth I],
RA [auth D],
S [auth A],
SA [auth D],
TA [auth D],
VC [auth J]
C H O3
Query on CL

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AD [auth K]
DB [auth E]
DC [auth H]
IA [auth C]
ID [auth L]
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]
Experimental Data & Validation

Experimental Data

  • 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
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

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
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description