6R3Y | pdb_00006r3y

M.tuberculosis nitrobindin with a cyanide molecule coordinated to the heme iron atom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.202 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Mycobacterial and Human Nitrobindins: Structure and Function.

De Simone, G.di Masi, A.Vita, G.M.Polticelli, F.Pesce, A.Nardini, M.Bolognesi, M.Ciaccio, C.Coletta, M.Turilli, E.S.Fasano, M.Tognaccini, L.Smulevich, G.Abbruzzetti, S.Viappiani, C.Bruno, S.Ascenzi, P.

(2020) Antioxid Redox Signal 33: 229-246

  • DOI: https://doi.org/10.1089/ars.2019.7874
  • Primary Citation Related Structures: 
    6R3W, 6R3Y

  • PubMed Abstract: 

    Aims: Nitrobindins (Nbs) are evolutionary conserved all-β-barrel heme-proteins displaying a highly solvent-exposed heme-Fe(III) atom. The physiological role(s) of Nbs is almost unknown. Here, the structural and functional properties of ferric Mycobacterium tuberculosis Nb ( Mt -Nb(III)) and ferric Homo sapiens Nb ( Hs -Nb(III)) have been investigated and compared with those of ferric Arabidopsis thaliana Nb ( At -Nb(III), Rhodnius prolixus nitrophorins ( Rp -NP(III)s), and mammalian myoglobins. Results: Data here reported demonstrate that Mt -Nb(III), At -Nb(III), and Hs -Nb(III) share with Rp -NP(III)s the capability to bind selectively nitric oxide, but display a very low reactivity, if any, toward histamine. Data obtained overexpressing Hs -Nb in human embryonic kidney 293 cells indicate that Hs -Nb localizes mainly in the cytoplasm and partially in the nucleus, thanks to a nuclear localization sequence encompassing residues Glu124-Leu154. Human Hs -Nb corresponds to the C -terminal domain of the human nuclear protein THAP4 suggesting that Nb may act as a sensor possibly modulating the THAP4 transcriptional activity residing in the N -terminal region. Finally, we provide strong evidence that both Mt -Nb(III) and Hs -Nb(III) are able to scavenge peroxynitrite and to protect free l-tyrosine against peroxynitrite-mediated nitration. Innovation: Data here reported suggest an evolutionarily conserved function of Nbs related to their role as nitric oxide sensors and components of antioxidant systems. Conclusion: Human THAP4 may act as a sensing protein that couples the heme-based Nb(III) reactivity with gene transcription. Mt -Nb(III) seems to be part of the pool of proteins required to scavenge reactive nitrogen and oxygen species produced by the host during the immunity response.


  • Organizational Affiliation
    • Dipartimento di Scienze, Università Roma Tre, Roma, Italy.

Macromolecule Content 

  • Total Structure Weight: 19.58 kDa 
  • Atom Count: 1,367 
  • Modeled Residue Count: 161 
  • Deposited Residue Count: 172 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
UPF0678 fatty acid-binding protein-like protein ERS007657_00996172Mycobacterium tuberculosisMutation(s): 0 
EC: 5.99
UniProt
Find proteins for P9WFG7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFG7 
Go to UniProtKB:  P9WFG7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WFG7
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.202 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.818α = 90
b = 74.383β = 90
c = 80.513γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-08
    Type: Initial release
  • Version 1.1: 2020-04-29
    Changes: Database references
  • Version 1.2: 2020-07-15
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-06
    Changes: Structure summary