6MNZ

Crystal structure of RibBX, a two domain 3,4-dihydroxy-2-butanone 4-phosphate synthase from A. baumannii.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.279 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Multi-metal Restriction by Calprotectin Impacts De Novo Flavin Biosynthesis in Acinetobacter baumannii.

Wang, J.Lonergan, Z.R.Gonzalez-Gutierrez, G.Nairn, B.L.Maxwell, C.N.Zhang, Y.Andreini, C.Karty, J.A.Chazin, W.J.Trinidad, J.C.Skaar, E.P.Giedroc, D.P.

(2019) Cell Chem Biol 26: 745

  • DOI: 10.1016/j.chembiol.2019.02.011
  • Primary Citation of Related Structures:  
    6MNZ

  • PubMed Abstract: 
  • Calprotectin (CP) inhibits bacterial viability through extracellular chelation of transition metals. However, how CP influences general metabolism remains largely unexplored. We show here that CP restricts bioavailable Zn and Fe to the pathogen Acinetobacter baumannii, inducing an extensive multi-metal perturbation of cellular physiology ...

    Calprotectin (CP) inhibits bacterial viability through extracellular chelation of transition metals. However, how CP influences general metabolism remains largely unexplored. We show here that CP restricts bioavailable Zn and Fe to the pathogen Acinetobacter baumannii, inducing an extensive multi-metal perturbation of cellular physiology. Proteomics reveals severe metal starvation, and a strain lacking the candidate Zn II metallochaperone ZigA possesses altered cellular abundance of multiple essential Zn-dependent enzymes and enzymes in de novo flavin biosynthesis. The ΔzigA strain exhibits decreased cellular flavin levels during metal starvation. Flavin mononucleotide provides regulation of this biosynthesis pathway, via a 3,4-dihydroxy-2-butanone 4-phosphate synthase (RibB) fusion protein, RibBX, and authentic RibB. We propose that RibBX ensures flavin sufficiency under CP-induced Fe limitation, allowing flavodoxins to substitute for Fe-ferredoxins as cell reductants. These studies elucidate adaptation to nutritional immunity and define an intersection between metallostasis and cellular metabolism in A. baumannii.


    Organizational Affiliation

    Department of Chemistry, Indiana University, Bloomington, IN 47405, USA; Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA. Electronic address: giedroc@indiana.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3,4-dihydroxy-2-butanone 4-phosphate synthaseA, B373Acinetobacter baumanniiMutation(s): 0 
Gene Names: 
EC: 4.1.99.12
UniProt
Find proteins for V5V8R9 (Acinetobacter baumannii)
Explore V5V8R9 
Go to UniProtKB:  V5V8R9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV5V8R9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.279 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.707α = 90
b = 136.857β = 98.527
c = 51.856γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR35 GM118157

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-05-29
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence