9K3C | pdb_00009k3c

Crystal Structure of CapA2 from Alistipes finegoldii in complex with PLP cofactor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 
    0.229 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


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Literature

Studies on Two Convergently Evolved Cysteate Synthases in Sulfonolipid Biosynthesis.

Yang, S.Wang, K.Hu, Y.Zhang, L.Zhang, C.Liu, Y.Li, Z.Jiang, L.Han, Y.Naowarojna, N.Wei, Y.Zhang, Y.

(2025) ACS Chem Biol 20: 2560-2573

  • DOI: https://doi.org/10.1021/acschembio.5c00142
  • Primary Citation Related Structures: 
    9K2P, 9K3C, 9K3O

  • PubMed Abstract: 

    Capnine-like sulfonolipids are sulfonate-containing analogs of sphingolipids found in many Bacteroidetes bacteria, where they govern essential functions such as gliding motility, outer membrane polysaccharide assembly, and antibiotic susceptibility. In gut-associated anaerobic Bacteroidetes, these sulfonolipids also modulate host-microbe interactions. In aerobic bacteria, the capnine precursor cysteate is produced by a pyridoxal phosphate (PLP)-dependent cysteate synthase (CapA1), a close homologue of cystathionine β-synthase (CBS). By contrast, the mechanism of cysteate production in anaerobic Bacteroidetes bacteria has not been biochemically studied. Herein, we report the characterizations of archaeal cysteate synthase homologue from the anaerobic bacteria Alistipes finegoldii ( Af CapA2). Biochemical assays confirm its ability to catalyze the conversion of O -phosphoserine (OPS) to cysteate. Crystal structures of Af CapA2 in complex with PLP and OPS-PLP identify essential catalytic residues and reveal a structural similarity to threonine synthase, unlike CapA1, which is more similar to CBS. Comparative analysis of CapA1 and this nonorthologous CapA2, including structural differences, catalytic versatility, and phylogenetic distribution across Bacteroidetes, suggests convergent evolution of cysteate synthase activity. Our work clarifies the details of sulfonolipid synthesis in anaerobic bacteria and the biochemical origins of this structurally distinctive lipid in the gut microbiome.


  • Organizational Affiliation
    • State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.

Macromolecule Content 

  • Total Structure Weight: 48.34 kDa 
  • Atom Count: 3,508 
  • Modeled Residue Count: 430 
  • Deposited Residue Count: 435 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cysteate synthase435Alistipes finegoldii DSM 17242Mutation(s): 0 
Gene Names: Alfi_3017
UniProt
Find proteins for I3YQJ3 (Alistipes finegoldii (strain DSM 17242 / JCM 16770 / CCUG 46020 / CIP 107999 / KCTC 15236 / AHN 2437))
Explore I3YQJ3 
Go to UniProtKB:  I3YQJ3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3YQJ3
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free:  0.229 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.821α = 90
b = 88.511β = 90
c = 95.117γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
PHENIXphasing
xia2data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-22
    Type: Initial release
  • Version 1.1: 2026-05-27
    Changes: Database references