7BVH

Crystal structure of arabinosyltransferase EmbC2-AcpM2 complex from Mycobacterium smegmatis complexed with di-arabinose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Structures of cell wall arabinosyltransferases with the anti-tuberculosis drug ethambutol.

Zhang, L.Zhao, Y.Gao, Y.Wu, L.Gao, R.Zhang, Q.Wang, Y.Wu, C.Wu, F.Gurcha, S.S.Veerapen, N.Batt, S.M.Zhao, W.Qin, L.Yang, X.Wang, M.Zhu, Y.Zhang, B.Bi, L.Zhang, X.Yang, H.Guddat, L.W.Xu, W.Wang, Q.Li, J.Besra, G.S.Rao, Z.

(2020) Science 368: 1211-1219

  • DOI: 10.1126/science.aba9102
  • Primary Citation of Related Structures:  
    7BVC, 7BVE, 7BVF, 7BVG, 7BVH

  • PubMed Abstract: 
  • The arabinosyltransferases EmbA, EmbB, and EmbC are involved in Mycobacterium tuberculosis cell wall synthesis and are recognized as targets for the anti-tuberculosis drug ethambutol. In this study, we determined cryo-electron microscopy and x-ray crystal structures of mycobacterial EmbA-EmbB and EmbC-EmbC complexes in the presence of their glycosyl donor and acceptor substrates and with ethambutol ...

    The arabinosyltransferases EmbA, EmbB, and EmbC are involved in Mycobacterium tuberculosis cell wall synthesis and are recognized as targets for the anti-tuberculosis drug ethambutol. In this study, we determined cryo-electron microscopy and x-ray crystal structures of mycobacterial EmbA-EmbB and EmbC-EmbC complexes in the presence of their glycosyl donor and acceptor substrates and with ethambutol. These structures show how the donor and acceptor substrates bind in the active site and how ethambutol inhibits arabinosyltransferases by binding to the same site as both substrates in EmbB and EmbC. Most drug-resistant mutations are located near the ethambutol binding site. Collectively, our work provides a structural basis for understanding the biochemical function and inhibition of arabinosyltransferases and the development of new anti-tuberculosis agents.


    Organizational Affiliation

    National Laboratory of Biomacromolecules and Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Integral membrane indolylacetylinositol arabinosyltransferase EmbCA, B1113Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: embCMSMEI_6219MSMEG_6387
EC: 2.4.2.34 (PDB Primary Data), 2.4.2 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for A0R612 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R612 
Go to UniProtKB:  A0R612
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R612
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Meromycolate extension acyl carrier proteinC, D99Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: acpMMSMEG_4326MSMEI_4226
UniProt
Find proteins for A0R0B3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R0B3 
Go to UniProtKB:  A0R0B3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R0B3
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranoseE, J 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G34232WB
GlyCosmos:  G34232WB
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose
F, G, H, I, K, L
F, G, H, I, K, L
2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G66120GK
GlyCosmos:  G66120GK
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900018
Query on PRD_900018
F, G, H, I, K, Lbeta-maltoseOligosaccharide / Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.08α = 90
b = 176.33β = 90
c = 207.77γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2017YFC0840300
National Science Foundation (NSF, China)China81520108019
Chinese Academy of SciencesChinaXDB29020000
Medical Research Council (MRC, United Kingdom)United KingdomMR/S000542/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-05-13
    Changes: Database references
  • Version 1.2: 2020-07-01
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary