7REF | pdb_00007ref

Structure of MS3494 from Mycobacterium smegmatis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.199 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.154 (Depositor) 
  • R-Value Observed: 
    0.158 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7REF

This is version 1.2 of the entry. See complete history

Literature

A periplasmic cinched protein is required for siderophore secretion and virulence of Mycobacterium tuberculosis.

Zhang, L.Kent, J.E.Whitaker, M.Young, D.C.Herrmann, D.Aleshin, A.E.Ko, Y.H.Cingolani, G.Saad, J.S.Moody, D.B.Marassi, F.M.Ehrt, S.Niederweis, M.

(2022) Nat Commun 13: 2255-2255

  • DOI: https://doi.org/10.1038/s41467-022-29873-6
  • Primary Citation Related Structures: 
    7REF

  • PubMed Abstract: 

    Iron is essential for growth of Mycobacterium tuberculosis, the causative agent of tuberculosis. To acquire iron from the host, M. tuberculosis uses the siderophores called mycobactins and carboxymycobactins. Here, we show that the rv0455c gene is essential for M. tuberculosis to grow in low-iron medium and that secretion of both mycobactins and carboxymycobactins is drastically reduced in the rv0455c deletion mutant. Both water-soluble and membrane-anchored Rv0455c are functional in siderophore secretion, supporting an intracellular role. Lack of Rv0455c results in siderophore toxicity, a phenotype observed for other siderophore secretion mutants, and severely impairs replication of M. tuberculosis in mice, demonstrating the importance of Rv0455c and siderophore secretion during disease. The crystal structure of a Rv0455c homolog reveals a novel protein fold consisting of a helical bundle with a 'cinch' formed by an essential intramolecular disulfide bond. These findings advance our understanding of the distinct M. tuberculosis siderophore secretion system.


  • Organizational Affiliation
    • Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.

Macromolecule Content 

  • Total Structure Weight: 31.03 kDa 
  • Atom Count: 2,298 
  • Modeled Residue Count: 245 
  • Deposited Residue Count: 254 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MS3494
A, B
127Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: ERS451418_03468
UniProt
Find proteins for A0QY10 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QY10 
Go to UniProtKB:  A0QY10
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0QY10
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BR

Query on BR



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.199 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.154 (Depositor) 
  • R-Value Observed: 0.158 (Depositor) 
Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.828α = 90
b = 98.828β = 90
c = 45.477γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-18
    Type: Initial release
  • Version 1.1: 2022-06-08
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary