6AHI

Crystal structure of O-acetylserine dependent cystathionine beta-synthase from Helicobacter pylori.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Identification and characterization of Helicobacter pylori O-acetylserine-dependent cystathionine beta-synthase, a distinct member of the PLP-II family.

Devi, S.Tarique, K.F.Ali, M.F.Abdul Rehman, S.A.Gourinath, S.

(2019) Mol Microbiol 112: 718-739

  • DOI: https://doi.org/10.1111/mmi.14315
  • Primary Citation of Related Structures:  
    6AHI

  • PubMed Abstract: 

    O-acetylserine sulfhydrylase (OASS) and cystathionine β-synthase (CBS) are members of the PLP-II family, and involved in L-cysteine production. OASS produces L-cysteine via a de novo pathway while CBS participates in the reverse transsulfuration pathway. O-acetylserine-dependent CBS (OCBS) was previously identified as a new member of the PLP-II family, which are predominantly seen in bacteria. The bacterium Helicobacter pylori possess only one OASS (hp0107) gene and we showed that the protein coded by this gene actually functions as an OCBS and utilizes L-homocysteine and O-acetylserine (OAS) to produce cystathionine. HpOCBS did not show CBS activity with the substrate L-serine and required OAS exclusively. The HpOCBS structure in complex with methionine showed a closed cleft state, explaining the initial mode of substrate binding. Sequence and structural analyses showed differences between the active sites of OCBS and CBS, and explain their different substrate preferences. We identified three hydrophobic residues near the active site of OCBS, corresponding to one serine and two tyrosine residues in CBSs. Mutational studies were performed on HpOCBS and Saccharomyces cerevisiae CBS. A ScCBS double mutant (Y158F/Y226V) did not display activity with L-serine, indicating indispensability of these polar residues for selecting substrate L-serine, however, did show activity with OAS.


  • Organizational Affiliation

    Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteine synthase
A, B
314Helicobacter pylori 26695Mutation(s): 0 
Gene Names: cysMcysKHP_0107
EC: 2.5.1.47
UniProt
Find proteins for P56067 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P56067 
Go to UniProtKB:  P56067
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56067
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MET
Query on MET

Download Ideal Coordinates CCD File 
C [auth B]METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
A, B
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.405α = 90
b = 82.719β = 90
c = 96.141γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2019-09-18
    Changes: Data collection, Database references
  • Version 1.2: 2022-04-27
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Refinement description