9K2P | pdb_00009k2p

The crystal structure of CapA1 from Capnocytophaga ochracea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 
    0.208 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9K2P

This is version 1.1 of the entry. See complete history

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: 74.16 kDa 
  • Atom Count: 5,842 
  • Modeled Residue Count: 666 
  • Deposited Residue Count: 666 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pyridoxal-5'-phosphate-dependent protein beta subunit
A, B
333Capnocytophaga ochracea DSM 7271Mutation(s): 0 
Gene Names: Coch_1829
EC: 2.5.1.76
UniProt
Find proteins for C7M8J5 (Capnocytophaga ochracea (strain ATCC 27872 / DSM 7271 / CCUG 9716 / JCM 12966 / NCTC 12371 / SS31 / VPI 2845))
Explore C7M8J5 
Go to UniProtKB:  C7M8J5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC7M8J5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free:  0.208 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.83α = 90
b = 107.11β = 90
c = 122.04γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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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