9JXU | pdb_00009jxu

Crystal structure of cysteine synthase A from Limosilactobacillus reuteri LR1 in its apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.271 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9JXU

This is version 1.3 of the entry. See complete history

Literature

Structure-Functional Examination of Cysteine Synthase A (CysK) from Limosilactobacillus reuteri LR1.

Pometun, A.A.Les, E.K.Chernobrovkina, A.V.Gorbovskaia, A.V.Chikurova, N.Y.Loginova, A.A.Antipov, A.N.Mordkovich, N.N.Shaposhnikov, L.A.Savin, S.S.Kleymenov, S.Y.Matyuta, I.O.Boyko, K.M.Minyaev, M.E.Hushpulian, D.M.Pometun, E.V.Tishkov, V.I.

(2025) Int J Mol Sci 27

  • DOI: https://doi.org/10.3390/ijms27010327
  • Primary Citation Related Structures: 
    9JXU

  • PubMed Abstract: 

    This study presents a comprehensive analysis of cysteine synthase A (CysK) from Limosilactobacillus reuteri LR1 (LreCysK), an enzyme involved in the biosynthesis of L-cysteine. This protein supports crucial cellular functions such as sulfur metabolism, antioxidant defense, detoxification, and protein synthesis. Previously, the gene encoding LreCysK was cloned, and the enzyme with His-tag on the N-terminus was obtained in active and soluble form. Here, kinetic parameters of the enzyme were determined by the previously developed high-pressure liquid chromatography (HPLC) and ninhydrin methods. It was found that LreCysK has similar K M OAS and k cat as CysKs from Escherichia coli and from the model plant Arabidopsis thaliana . The thermal stability of LreCysK was studied using differential scanning calorimetry. It was revealed that the melting point of the enzyme increases to almost 90°C when Pyridoxal-5 phosphate (PLP) is added, indicating that the stability of the enzyme complex with PLP is relatively high. Structural studies revealed that LreCysK is a dimer, and its active site is similar to those of other enzymes, but exhibits some features characteristic of lactobacilli CysKs (GISA), as well as unique residues, such as Ile50. Also, the potential biotechnological applications of LreCysK are discussed. These findings enhance our understanding of LreCysK's biochemical versatility and its potential applications in biotechnology and medicine.


  • Organizational Affiliation
    • Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Avenue, 119071 Moscow, Russia.

Macromolecule Content 

  • Total Structure Weight: 67.34 kDa 
  • Atom Count: 4,121 
  • Modeled Residue Count: 555 
  • Deposited Residue Count: 626 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cysteine synthase
A, B
313Limosilactobacillus reuteriMutation(s): 0 
Gene Names: cysKB1A73_08060B5F04_07160B5G22_06315GTO86_10515
EC: 2.5.1.47

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE

Query on PGE



Download:Ideal Coordinates CCD File
C [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
E [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
J [auth A],
K [auth A],
L [auth A],
N [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
D [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
D [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
M [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.271 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.642α = 90
b = 101.292β = 107.33
c = 63.53γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
CrysalisProdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-13
    Type: Initial release
  • Version 1.1: 2024-12-25
    Changes: Structure summary
  • Version 1.2: 2025-10-22
    Changes: Structure summary
  • Version 1.3: 2026-01-21
    Changes: Database references