Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 38.93 kDa 
• Atom Count: 2872 
• Modelled Residue Count: 334 
• Deposited Residue Count: 339 
• Unique protein chains: 1

4MP6

Staphyloferrin B precursor biosynthetic enzyme SbnB bound to citrate and NAD+

• PDB DOI: 10.2210/pdb4MP6/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Staphylococcus aureus subsp. aureus MW2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-09-12 Released: 2014-03-05 
• Deposition Author(s): Grigg, J.C., Kobylarz, M.J., Rai, D.K., Murphy, M.E.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.239 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 

Literature

Synthesis of L-2,3-diaminopropionic Acid, a siderophore and antibiotic precursor.

Kobylarz, M.J., Grigg, J.C., Takayama, S.J., Rai, D.K., Heinrichs, D.E., Murphy, M.E.

(2014) Chem Biol 21: 379-388

• PubMed: 24485762 
• DOI: 10.1016/j.chembiol.2013.12.011
• Primary Citation of Related Structures:  
  4M54, 4MP3, 4MP6, 4MP8, 4MPD


• PubMed Abstract: 
  

L-2,3-diaminopropionic acid (L-Dap) is an amino acid that is a precursor of antibiotics and staphyloferrin B a siderophore produced by Staphylococcus aureus. SbnA and SbnB are encoded by the staphyloferrin B biosynthetic gene cluster and are implicated in L-Dap biosynthesis. We demonstrate here that SbnA uses PLP and substrates O-phospho-L-serine and L-glutamate to produce a metabolite N-(1-amino-1-carboxyl-2-ethyl)-glutamic acid (ACEGA). SbnB is shown to use NAD(+) to oxidatively hydrolyze ACEGA to yield α-ketoglutarate and L-Dap. Also, we describe crystal structures of SbnB in complex with NADH and ACEGA as well as with NAD(+) and α-ketoglutarate to reveal the residues required for substrate binding, oxidation, and hydrolysis. SbnA and SbnB contribute to the iron sparing response of S. aureus that enables staphyloferrin B biosynthesis in the absence of an active tricarboxylic acid cycle.

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Organizational Affiliation: 

Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative ornithine cyclodeaminase	A	339	Staphylococcus aureus subsp. aureus MW2	Mutation(s): 0  Gene Names: sbnB
UniProt
Find proteins for A0A0H3K9Y6 (Staphylococcus aureus (strain Newman)) Explore A0A0H3K9Y6  Go to UniProtKB:  A0A0H3K9Y6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
CIT	C [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.239 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.66	α = 90
b = 62.66	β = 90
c = 157.079	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-09-12 
• Released Date: 2014-03-05 
Deposition Author(s): Grigg, J.C., Kobylarz, M.J., Rai, D.K., Murphy, M.E.P.

Revision History  

• Version 1.0: 2014-03-05
  Type: Initial release
  
• Version 1.1: 2014-04-09
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description