3OXH

Mycobacterium tuberculosis kinase inhibitor homolog RV0577


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural and Biophysical Characterization of the Mycobacterium tuberculosis Protein Rv0577, a Protein Associated with Neutral Red Staining of Virulent Tuberculosis Strains and Homologue of the Streptomyces coelicolor Protein KbpA.

Buchko, G.W.Echols, N.Flynn, E.M.Ng, H.L.Stephenson, S.Kim, H.B.Myler, P.J.Terwilliger, T.C.Alber, T.Kim, C.Y.

(2017) Biochemistry 

  • DOI: 10.1021/acs.biochem.7b00511
  • Primary Citation of Related Structures:  
    3OXH

  • PubMed Abstract: 
  • Mycobacterium tuberculosis protein Rv0577 is a prominent antigen in tuberculosis patients, the component responsible for neutral red staining of virulent strains of M. tuberculosis, a putative component in a methylglyoxal detoxification pathway, and an agonist of toll-like receptor 2 ...

    Mycobacterium tuberculosis protein Rv0577 is a prominent antigen in tuberculosis patients, the component responsible for neutral red staining of virulent strains of M. tuberculosis, a putative component in a methylglyoxal detoxification pathway, and an agonist of toll-like receptor 2. It also has an amino acid sequence that is 36% identical to that of Streptomyces coelicolor AfsK-binding protein A (KbpA), a component in the complex secondary metabolite pathways in the Streptomyces genus. To gain insight into the biological function of Rv0577 and the family of KpbA kinase regulators, the crystal structure for Rv0577 was determined to a resolution of 1.75 Å, binding properties with neutral red and deoxyadenosine were surveyed, backbone dynamics were measured, and thermal stability was assayed by circular dichroism spectroscopy. The protein is composed of four approximate repeats with a βαβββ topology arranged radially in consecutive pairs to form two continuous eight-strand β-sheets capped on both ends with an α-helix. The two β-sheets intersect in the center at roughly a right angle and form two asymmetric deep "saddles" that may serve to bind ligands. Nuclear magnetic resonance chemical shift perturbation experiments show that neutral red and deoxyadenosine bind to Rv0577. Binding to deoxyadenosine is weaker with an estimated dissociation constants of 4.1 ± 0.3 mM for saddle 1. Heteronuclear steady-state { 1 H}- 15 N nuclear Overhauser effect, T 1 , and T 2 values were generally uniform throughout the sequence with only a few modest pockets of differences. Circular dichroism spectroscopy characterization of the thermal stability of Rv0577 indicated irreversible unfolding upon heating with an estimated melting temperature of 56 °C.


    Organizational Affiliation

    Bioscience Division, Los Alamos National Laboratory , Los Alamos, New Mexico 87545, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RV0577 PROTEINA282Mycobacterium tuberculosisMutation(s): 0 
Gene Names: cfp30BMT0606MTV039.15Rv0577TB27.3
UniProt
Find proteins for P9WIR3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WIR3 
Go to UniProtKB:  P9WIR3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PMB (Subject of Investigation/LOI)
Query on PMB

Download Ideal Coordinates CCD File 
D [auth A]PARA-MERCURY-BENZENESULFONIC ACID
C6 H5 Hg O3 S
KQAOIKIZSJJTII-UHFFFAOYSA-N
 Ligand Interaction
XYL (Subject of Investigation/LOI)
Query on XYL

Download Ideal Coordinates CCD File 
E [auth A]Xylitol
C5 H12 O5
HEBKCHPVOIAQTA-SCDXWVJYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.597α = 90
b = 81.981β = 90
c = 36.037γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
REFMACrefinement
ADSCdata collection
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-19
    Type: Initial release
  • Version 1.1: 2011-11-23
    Changes: Other
  • Version 1.2: 2017-08-09
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Database references, Derived calculations, Structure summary