7CYR

The closed conformation of MSMEG_1954 from Mycobacterium smegmatis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Conformational Changes in a Macrolide Antibiotic Binding Protein From Mycobacterium smegmatis Upon ADP Binding.

Zhang, Q.Liu, X.Liu, H.Zhang, B.Yang, H.Mi, K.Guddat, L.W.Rao, Z.

(2021) Front Microbiol 12: 780954-780954

  • DOI: 10.3389/fmicb.2021.780954
  • Primary Citation of Related Structures:  
    7CY2, 7CYR, 7CZ2

  • PubMed Abstract: 
  • Rv3197 (MABP-1), a non-canonical ABC protein in Mycobacterium tuberculosis , has ATPase activity and confers inducible resistance to the macrolide family of antibiotics. Here we have shown that MSMEG_1954, the homolog of Rv3197 in M. smegmatis , has a similar function of conferring macrolide resistance ...

    Rv3197 (MABP-1), a non-canonical ABC protein in Mycobacterium tuberculosis , has ATPase activity and confers inducible resistance to the macrolide family of antibiotics. Here we have shown that MSMEG_1954, the homolog of Rv3197 in M. smegmatis , has a similar function of conferring macrolide resistance. Crystal structures of apo-MSMEG_1954 (form1 and form 2) and MSMEG_1954 in complex with ADP have been determined. These three structures show that MSMEG_1954 has at least two different conformations we identify as closed state (MSMEG_1954-form 1) and open state (MSMEG_1954-form 2 and MSMEG_1954-ADP). Structural superimposition shows that the MSMEG_1954-form 2 and MSMEG_1954-ADP complex have similar conformation to that observed for MABP-1 and MABP-1-erythromicin complex structure. However, the antibiotic binding pocket in MSMEG_1954-form 1 is completely blocked by the N-terminal accessory domain. When bound by ADP, the N-terminal accessory domain undergoes conformational change, which results in the open of the antibiotic binding pocket. Because of the degradation of N terminal accessory domain in MSMSG_1954-form 2, it is likely to represent a transitional state between MSMEG_1954-form 1 and MSMEG_1954-ADP complex structure.


    Organizational Affiliation

    Laboratory of Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ABC1 family proteinA439Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_1954
UniProt
Find proteins for A0QTT2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QTT2 
Go to UniProtKB:  A0QTT2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0QTT2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download Ideal Coordinates CCD File 
B [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.574α = 90
b = 61.236β = 90
c = 117.25γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81520108019

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-08
    Type: Initial release
  • Version 1.1: 2022-02-23
    Changes: Database references