8JUI

Crystal structures of Cystathionine beta lyase from Bacillus cereus ATCC 14579


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal structures of cystathionine beta-lyase and cystathionine beta-lyase like protein from Bacillus cereus ATCC 14579.

Lee, S.H.Yu, H.Hong, J.Seok, J.Kim, K.J.

(2024) Biochem Biophys Res Commun 742: 151122-151122

  • DOI: https://doi.org/10.1016/j.bbrc.2024.151122
  • Primary Citation of Related Structures:  
    8JUI, 8JUJ

  • PubMed Abstract: 

    Cystathionine β-lyase (CBL) and cystathionine β-lyase-like protein (CBLP) are key PLP-dependent enzymes involved in methionine biosynthesis. In Bacillus cereus ATCC 14579 CBL (BcCBL) and CBLP (BcCBLP) catalyze the conversion of cystathionine to homocysteine and pyruvate. In this study, we found that both BcCBL and BcCBLP effectively catalyze cystathionine cleavage, with BcCBLP exhibiting a higher catalytic efficiency (kcat) and low substrate affinity (K m ). We determined their crystal structures in complex with pyridoxal phosphate (PLP). BcCBL, forming a tetramer, aligns with typical CBLs in sulfur amino acid metabolism, while BcCBLP, forming a dimer, resembles the bifunctional MalY enzyme from Escherichia coli, indicating potential additional regulatory roles. These structural and functional insights highlight the distinct roles of BcCBL and BcCBLP in cellular metabolism. This study provides valuable insights into the structural diversity and potential functions of these enzymes, contributing to the broader knowledge of PLP-dependent enzymatic mechanisms.


  • Organizational Affiliation

    KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cystathionine beta-lyase395Bacillus cereus ATCC 14579Mutation(s): 0 
Gene Names: BC_4254
EC: 4.4.1.8
UniProt
Find proteins for Q818J6 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711))
Explore Q818J6 
Go to UniProtKB:  Q818J6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ818J6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
A
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.1α = 90
b = 143.1β = 90
c = 80.907γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-03
    Type: Initial release
  • Version 2.0: 2024-12-18
    Changes: Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Structure summary