7BVC

Cryo-EM structure of Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with ethambutol


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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 EmbAA1,088Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: embAMSMEG_6388
EC: 2.4.2
Membrane Entity: Yes 
UniProt
Find proteins for A0R613 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R613 
Go to UniProtKB:  A0R613
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R613
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Integral membrane indolylacetylinositol arabinosyltransferase EmbBB1,100Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: embBMSMEI_6221MSMEG_6389
EC: 2.4.2.34 (PDB Primary Data), 2.4.2 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for A0R614 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R614 
Go to UniProtKB:  A0R614
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R614
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Meromycolate extension acyl carrier proteinC [auth P]99Mycolicibacterium 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
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
F8L (Subject of Investigation/LOI)
Query on F8L

Download Ideal Coordinates CCD File 
E [auth A][(2Z,6E,10E,14Z,18E,22Z,26Z)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaenyl] [(2S,3S,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl] hydrogen phosphate
C55 H91 O8 P
YRIPSPRNAZBQAG-KAKITAEPSA-N
 Ligand Interaction
PNS (Subject of Investigation/LOI)
Query on PNS

Download Ideal Coordinates CCD File 
G [auth B]4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N
 Ligand Interaction
95E
Query on 95E

Download Ideal Coordinates CCD File 
I [auth B]Ethambutol
C10 H24 N2 O2
AEUTYOVWOVBAKS-UWVGGRQHSA-N
 Ligand Interaction
PO4
Query on PO4

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H [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaXDB29020000
National Natural Science Foundation of China (NSFC)China81520108019
Ministry of Science and Technology (MoST, China)China2017YFC0840300
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