6O0A

Crystal structure of flavohemoglobin from Malassezia yamatoensis with bound FAD and heme determined by iron SAD phasing


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

HGT in the human and skin commensal Malassezia : A bacterially derived flavohemoglobin is required for NO resistance and host interaction.

Ianiri, G.Coelho, M.A.Ruchti, F.Sparber, F.McMahon, T.J.Fu, C.Bolejack, M.Donovan, O.Smutney, H.Myler, P.Dietrich, F.Fox 3rd, D.LeibundGut-Landmann, S.Heitman, J.

(2020) Proc Natl Acad Sci U S A 117: 15884-15894

  • DOI: https://doi.org/10.1073/pnas.2003473117
  • Primary Citation of Related Structures:  
    6O0A

  • PubMed Abstract: 

    The skin of humans and animals is colonized by commensal and pathogenic fungi and bacteria that share this ecological niche and have established microbial interactions. Malassezia are the most abundant fungal skin inhabitant of warm-blooded animals and have been implicated in skin diseases and systemic disorders, including Crohn's disease and pancreatic cancer. Flavohemoglobin is a key enzyme involved in microbial nitrosative stress resistance and nitric oxide degradation. Comparative genomics and phylogenetic analyses within the Malassezia genus revealed that flavohemoglobin-encoding genes were acquired through independent horizontal gene transfer events from different donor bacteria that are part of the mammalian microbiome. Through targeted gene deletion and functional complementation in Malassezia sympodialis , we demonstrated that bacterially derived flavohemoglobins are cytoplasmic proteins required for nitric oxide detoxification and nitrosative stress resistance under aerobic conditions. RNA-sequencing analysis revealed that endogenous accumulation of nitric oxide resulted in up-regulation of genes involved in stress response and down-regulation of the MalaS7 allergen-encoding genes. Solution of the high-resolution X-ray crystal structure of Malassezia flavohemoglobin revealed features conserved with both bacterial and fungal flavohemoglobins. In vivo pathogenesis is independent of Malassezia flavohemoglobin. Lastly, we identified an additional 30 genus- and species-specific horizontal gene transfer candidates that might have contributed to the evolution of this genus as the most common inhabitants of animal skin.


  • Organizational Affiliation

    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Flavohemoglobin413Malassezia yamatoensisMutation(s): 0 
UniProt
Find proteins for A0A4V8H045 (Malassezia yamatoensis)
Explore A0A4V8H045 
Go to UniProtKB:  A0A4V8H045
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4V8H045
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
MPD
Query on MPD

Download Ideal Coordinates CCD File 
D [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.01α = 90
b = 110.6β = 90
c = 39.01γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 1.1: 2022-03-23
    Changes: Database references