9JQF | pdb_00009jqf

Crystal structure of the CJ0600 protein from Campylobacter jejuni


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.206 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: in silico
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Literature

Structural analysis of the CJ0600 protein from Campylobacter jejuni.

Ki, D.U.Choi, H.J.Song, W.S.Yoon, S.I.

(2024) Biochem Biophys Res Commun 735: 150810-150810

  • DOI: https://doi.org/10.1016/j.bbrc.2024.150810
  • Primary Citation of Related Structures:  
    9JQF

  • PubMed Abstract: 

    The Campylobacter jejuni bacterium, which causes foodborne enteritis in humans, expresses the uncharacterized protein CJ0600. Based on sequence analysis, CJ0600 has been proposed to function as a 1-aminocyclopropane-1-carboxylate (ACC) deaminase (AccDA) or cysteine desulfhydrase (CysDS). However, it has never been investigated whether CJ0600 exerts AccDA or CysDS activity or how CJ0600 mediates its enzymatic activity. To reveal the structural features necessary for the function of CJ0600, we determined the crystal structure of CJ0600 and characterized its enzymatic activity. CJ0600 contains two domains and features an interdomain pocket, which accommodates a pyridoxal 5'-phosphate (PLP) molecule as a Schiff base with its lysine residue (K35), as observed in its structural homologs, including AccDA, CysDS, and serine deaminase (SerDA). However, unlike its structural homologs, CJ0600 exists as a monomer and exhibits unique structural features throughout its structure. Moreover, CJ0600 contains unique active site residues that are not observed in AccDA, CysDS, or SerDA. Consistently, phylogenetic analysis indicates that CJ0600 and its orthologs are evolutionarily distinct from AccDA, CysDS, and SerDA. Indeed, CJ0600 showed no CysDS or SerDA activity and extremely weak AccDA activity. These observations suggest that CJ0600 functions as a unique PLP-dependent enzyme that has not been reported.


  • Organizational Affiliation
    • Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
1-aminocyclopropane-1-carboxylate deaminase/D-cysteine desulfhydrase297Campylobacter jejuniMutation(s): 0 
Gene Names: F0E97_00965FZK63_02140QE916_000133
UniProt
Find proteins for A0A5Z1H273 (Campylobacter jejuni)
Explore A0A5Z1H273 
Go to UniProtKB:  A0A5Z1H273
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5Z1H273
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.206 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.748α = 90
b = 122.748β = 90
c = 104.691γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfRS-2023-00208153

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release