Crystal structure of SbnH in complex with citryl-diaminoethane

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 

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Structural Insights into Substrate Recognition and Activity Regulation of the Key Decarboxylase SbnH in Staphyloferrin B Biosynthesis.

Tang, J.Ju, Y.Gu, Q.Xu, J.Zhou, H.

(2019) J Mol Biol 431: 4868-4881

  • DOI: https://doi.org/10.1016/j.jmb.2019.10.009
  • Primary Citation of Related Structures:  
    6KNH, 6KNI, 6KNK

  • PubMed Abstract: 

    Staphyloferrin B is a hydroxycarboxylate siderophore that is crucial for the invasion and virulence of Staphylococcus aureus in mammalian hosts where free iron ions are scarce. The assembly of staphyloferrin B involves four enzymatic steps, in which SbnH, a pyridoxal 5'-phosphate (PLP)-dependent decarboxylase, catalyzes the second step. Here, we report the X-ray crystal structures of S. aureus SbnH (SaSbnH) in complex with PLP, citrate, and the decarboxylation product citryl-diaminoethane (citryl-Dae). The overall structure of SaSbnH resembles those of the previously reported PLP-dependent amino acid decarboxylases, but the active site of SaSbnH showed unique structural features. Structural and mutagenesis analysis revealed that the citryl moiety of the substrate citryl-l-2,3-diaminopropionic acid (citryl-l-Dap) inserts into a narrow groove at the dimer interface of SaSbnH and forms hydrogen bonding interactions with both subunits. In the active site, a conserved lysine residue forms an aldimine linkage with the cofactor PLP, and a phenylalanine residue is essential for accommodating the l-configuration Dap of the substrate. Interestingly, the freestanding citrate molecule was found to bind to SaSbnH in a conformation inverse to that of the citryl group of citryl-Dae and efficiently inhibit SaSbnH. As an intermediate in the tricarboxylic acid (TCA) cycle, citrate is highly abundant in bacterial cells until iron depletion; thus, its inhibition of SaSbnH may serve as an iron-dependent regulatory mechanism in staphyloferrin B biosynthesis.

  • Organizational Affiliation

    Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable diaminopimelate decarboxylase protein
A, B, C
406Staphylococcus aureus subsp. aureus Mu50Mutation(s): 1 
Gene Names: SAV0123
Find proteins for A0A0H3JPF2 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore A0A0H3JPF2 
Go to UniProtKB:  A0A0H3JPF2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3JPF2
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DN9 (Subject of Investigation/LOI)
Query on DN9

Download Ideal Coordinates CCD File 
D [auth A](2~{S})-2-[2-[2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]ethylamino]-2-oxidanylidene-ethyl]-2-oxidanyl-butanedioic acid
C16 H24 N3 O11 P
X3J (Subject of Investigation/LOI)
Query on X3J

Download Ideal Coordinates CCD File 
C8 H14 N2 O6
Query on PO4

Download Ideal Coordinates CCD File 
E [auth B],
G [auth C]
O4 P
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.299α = 90
b = 80.325β = 102.07
c = 111.524γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2017YFE0109900
National Natural Science Foundation of ChinaChinaNo. 81773636

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description