4I42 | pdb_00004i42

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

• PDB DOI: https://doi.org/10.2210/pdb4I42/pdb

• Classification: LYASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-11-27 Released: 2013-05-08 
• Deposition Author(s): Sun, Y., Song, H., Li, J., Li, Y., Jiang, M., Zhou, J., Guo, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.182 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

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

• PubMed: 23658663 
• DOI: https://doi.org/10.1371/journal.pone.0063095
• Primary Citation 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.

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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.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 397.46 kDa 
• Atom Count: 30,129 
• Modeled Residue Count: 3,398 
• Deposited Residue Count: 3,420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1,4-Dihydroxy-2-naphthoyl-CoA synthase	A, B, C, D, E, F, G, H, I, J, K, L	285	Escherichia coli K-12	Mutation(s): 0  Gene Names: b2262, JW2257, menB EC: 4.1.3.36
UniProt
Find proteins for P0ABU0 (Escherichia coli (strain K12)) Explore P0ABU0  Go to UniProtKB:  P0ABU0

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1HA	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
BTB	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
PEG	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
SO4	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
GOL	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
EDO	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
BCT	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
CL	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.182 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.646	α = 90
b = 141.659	β = 90
c = 288.477	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-08 
Deposition Author(s): Sun, Y., Song, H., Li, J., Li, Y., Jiang, M., Zhou, J., Guo, Z.

Revision History  

• 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