7C9K

Crystal Structure of E84Q mutant of CntL in complex with SAM

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.260 

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Literature

Structural insights into the ligand recognition and catalysis of the key aminobutanoyltransferase CntL in staphylopine biosynthesis.

Luo, Z., Luo, S., Ju, Y., Ding, P., Xu, J., Gu, Q., Zhou, H.

(2021) FASEB J 35: e21575-e21575

  • DOI: 10.1096/fj.202002287RR
  • Primary Citation of Related Structures:  
    7C7M, 7C9K, 7C9M

  • PubMed Abstract: 

    • Staphylopine (StP) and other nicotianamine-like metallophores are crucial for many pathogens to acquire the transition metals from hosts during invasion. CntL from Staphylococcus aureus (SaCntL) catalyzes the condensation of the 2-aminobutyrate (Ab) moiety of S-adenosylmethionine (SAM) with D-histidine in the biosynthesis of StP ...

    Staphylopine (StP) and other nicotianamine-like metallophores are crucial for many pathogens to acquire the transition metals from hosts during invasion. CntL from Staphylococcus aureus (SaCntL) catalyzes the condensation of the 2-aminobutyrate (Ab) moiety of S-adenosylmethionine (SAM) with D-histidine in the biosynthesis of StP. Here, we report the crystal structures of SaCntL in complex with either SAM or two products. The structure of SaCntL consists of an N-terminal four-helix bundle (holding catalytic residue E84) and a C-terminal Rossmann fold (binding the substrates). The sequence connecting the N- and C-terminal domains (N-C linker) in SaCntL was found to undergo conformational alternation between open and closed states. Our structural and biochemical analyses suggested that this intrinsically dynamic interdomain linker forms an additional structural module that plays essential roles in ligand diffusion, recognition, and catalysis. We confirmed that SaCntL stereoselectively carries out the catalysis of D-His but not its enantiomer, L-His, and we found that the N-C linker and active site of SaCntL could accommodate both enantiomers. SaCntL is likely able to bind L-His without catalysis, and as a result, L-His could show inhibitory effects toward SaCntL. These findings provide critical structural and mechanistic insights into CntL, which facilitates a better understanding of the biosynthesis of nicotianamine-like metallophores and the discovery of inhibitors of this process.

    Organizational Affiliation: 

    Research Center for Drug Discovery and Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-histidine 2-aminobutanoyltransferaseA, B280Staphylococcus aureus subsp. aureus Mu50Mutation(s): 0 
Gene Names: cntL, SAV2469
EC: 2.5.1.152
UniProt
Find proteins for A0A0H3JXA8 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore A0A0H3JXA8 
Go to UniProtKB:  A0A0H3JXA8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3JXA8
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.260 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.816α = 90
b = 133.21β = 90
c = 135.278γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-06-06 
  • Released Date: 2021-04-28 
    • Deposition Author(s): Luo, Z., Zhou, H.
Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81773636

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-28
    Type: Initial release