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 

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The arabinosyltransferases EmbA, EmbB, and EmbC are involved in Mycobacterium tuberculosis cell wall synthesis and are recognized as the targets for the anti-tuberculosis drug ethambutol. We have determined cryo-electron microscopy and x-ray ...

    The arabinosyltransferases EmbA, EmbB, and EmbC are involved in Mycobacterium tuberculosis cell wall synthesis and are recognized as the targets for the anti-tuberculosis drug ethambutol. We have 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 by binding to the same site as both substrates in EmbB and EmbC. The majority of drug-resistant mutations are located nearby to the ethambutol-binding site. Collectively, our work provides a structural basis for understanding the biochemical function and inhibition of arabinosyltransferases and 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
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)
Find proteins for A0R612 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R612 
Go to UniProtKB:  A0R612
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Meromycolate extension acyl carrier proteinC, D99Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: acpMMSMEG_4326MSMEI_4226
Find proteins for A0R0B3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R0B3 
Go to UniProtKB:  A0R0B3
Protein Feature View
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  • Reference Sequence
Oligosaccharides
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose
E, J
2 N/A
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose
F, G, H, I, K, L
2 N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BXY
Query on BXY

Download CCD File 
A, B
alpha-D-arabinofuranose
C5 H10 O5
HMFHBZSHGGEWLO-MBMOQRBOSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 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

View Full Validation Report



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 

  • 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