8KIF

The structure of MmaE with substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Variation in biosynthesis and metal-binding properties of isonitrile-containing peptides produced by Mycobacteria versus Streptomyces.

Chen, T.Y.Chen, J.Ruszczycky, M.W.Hilovsky, D.Hostetler, T.Liu, X.Zhou, J.Chang, W.C.

(2024) ACS Catal 14: 4975-4983

  • DOI: https://doi.org/10.1021/acscatal.4c00645
  • Primary Citation of Related Structures:  
    8KHT, 8KIF

  • PubMed Abstract: 

    A number of bacteria are known to produce isonitrile-containing peptides (INPs) that facilitate metal transport and are important for cell survival; however, considerable structural variation is observed among INPs depending on the producing organism. While non-heme iron 2-oxoglutarate dependent isonitrilases catalyze isonitrile formation, how the natural variation in INP structure is controlled and its implications for INP bioactivity remain open questions. Herein, total chemical synthesis is utilized with X-Ray crystallographic analysis of mycobacterial isonitrilases to provide a structural model of substrate specificity that explains the longer alkyl chains observed in mycobacterial versus Streptomyces INPs. Moreover, proton NMR titration experiments demonstrate that INPs regardless of alkyl chain length are specific for binding copper instead of zinc. These results suggest that isonitrilases may act as gatekeepers in modulating the observed biological distribution of INP structures and this distribution may be primarily related to differing metal transport requirements among the producing strains.


  • Organizational Affiliation

    Department of Chemistry, North Carolina State University, Raleigh, NC 27695, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative dioxygenaseA [auth B],
B [auth A],
C,
D
305Mycobacterium marinum MMutation(s): 0 
Gene Names: MMRN_02610
UniProt
Find proteins for B2HKM3 (Mycobacterium marinum (strain ATCC BAA-535 / M))
Explore B2HKM3 
Go to UniProtKB:  B2HKM3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2HKM3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.822α = 82.814
b = 77.951β = 78.341
c = 99.833γ = 75.588
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2018YFA0901900

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release
  • Version 1.1: 2024-07-03
    Changes: Database references