6MNZ | pdb_00006mnz

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

• PDB DOI: https://doi.org/10.2210/pdb6MNZ/pdb

• Classification: LYASE
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2018-10-03 Released: 2019-04-17 
• Deposition Author(s): Wang, J., Gonzalez-Gutierrez, G., Giedroc, D.P.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 
  0.303 (Depositor), 0.303 (DCC) 
• R-Value Work: 
  0.278 (Depositor), 0.278 (DCC) 
• R-Value Observed: 
  0.279 (Depositor) 

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

• PubMed: 30905682 
• DOI: https://doi.org/10.1016/j.chembiol.2019.02.011
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Department of Chemistry, Indiana University, Bloomington, IN 47405, USA; Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.
Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.
Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA.
Department of Chemistry, Indiana University, Bloomington, IN 47405, USA; Laboratory for Biological Mass Spectrometry, Department of Chemistry, Indiana University, Bloomington, IN 47405, USA.
Magnetic Resonance Centre (CERM), University of Florence, Florence, 50019 Sesto Fiorentino, Italy.
Department of Chemistry, Indiana University, Bloomington, IN 47405, USA.
Department of Chemistry, Indiana University, Bloomington, IN 47405, USA; Laboratory for Biological Mass Spectrometry, Department of Chemistry, Indiana University, Bloomington, IN 47405, USA. Electronic address: [e-mail].
Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA. Electronic address: [e-mail].
Department of Chemistry, Indiana University, Bloomington, IN 47405, USA; Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 82.84 kDa 
• Atom Count: 5,339 
• Modeled Residue Count: 672 
• Deposited Residue Count: 746 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3,4-dihydroxy-2-butanone 4-phosphate synthase	A, B	373	Acinetobacter baumannii	Mutation(s): 0  Gene Names:  ribB, ribBA, A7M79_16415, A7M90_07480, A7N09_07660, AB895_1395, APD06_16235, AZE33_19550, B4R90_18035, BGC29_12000, BWP00_07280, C2U32_13770, CAS83_08960, CBE85_14000, CHQ89_12900, CPI82_04655, IX87_13995, LV38_00273 EC: 4.1.99.12
UniProt
Find proteins for V5V8R9 (Acinetobacter baumannii) Explore V5V8R9  Go to UniProtKB:  V5V8R9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	G [auth A], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free:  0.303 (Depositor), 0.303 (DCC) 
• R-Value Work:  0.278 (Depositor), 0.278 (DCC) 
• R-Value Observed: 0.279 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.707	α = 90
b = 136.857	β = 98.527
c = 51.856	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-04-17 
Deposition Author(s): Wang, J., Gonzalez-Gutierrez, G., Giedroc, D.P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	R35 GM118157

Revision History  

• 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
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Refinement description