4QIJ

Crystal structure of MenB from Mycobacteria tuberculosis in complex with 1-HNA-CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.127 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Ligand-dependent active-site closure revealed in the crystal structure of Mycobacterium tuberculosis MenB complexed with product analogues

Song, H.Sung, H.P.Tse, Y.S.Jiang, M.Guo, Z.H.

(2014) Acta Crystallogr.,Sect.D 70: 2959-2969

  • DOI: 10.1107/S1399004714019440
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 1,4-Dihydroxy-2-naphthoyl coenzyme A (DHNA-CoA) synthase catalyzes an essential intramolecular Claisen condensation in menaquinone biosynthesis and is an important target for the development of new antibiotics. This enzyme in Mycobacterium tuberculos ...

    1,4-Dihydroxy-2-naphthoyl coenzyme A (DHNA-CoA) synthase catalyzes an essential intramolecular Claisen condensation in menaquinone biosynthesis and is an important target for the development of new antibiotics. This enzyme in Mycobacterium tuberculosis is cofactor-free and is classified as a type II DHNA-CoA synthase, differing from type I enzymes, which rely on exogenous bicarbonate for catalysis. Its crystal structures in complex with product analogues have been determined at high resolution to reveal ligand-dependent structural changes, which include the ordering of a 27-residue active-site loop (amino acids 107-133) and the reorientation of the carboxy-terminal helix (amino acids 289-301) that forms part of the active site from the opposing subunit across the trimer-trimer interface. These structural changes result in closure of the active site to the bulk solution, which is likely to take place through an induced-fit mechanism, similar to that observed for type I DHNA-CoA synthases. These findings demonstrate that the ligand-dependent conformational changes are a conserved feature of all DHNA-CoA synthases, providing new insights into the catalytic mechanism of this essential tubercular enzyme.


    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, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1,4-Dihydroxy-2-naphthoyl-CoA synthase
A, B, C, D, E, F, G, H, I, J, K, L
334Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: menB
EC: 4.1.3.36
Find proteins for P9WNP5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WNP5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1HA
Query on 1HA

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
1-hydroxy-2-naphthoyl-CoA
C32 H42 N7 O18 P3 S
ZHSLHXZSNOSMQG-HSJNEKGZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1HAKd: 2900 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.127 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 91.498α = 90.00
b = 148.315β = 103.47
c = 140.999γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MOSFLMdata reduction
HKL-2000data collection
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-19
    Type: Initial release