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TitleConformational Snapshots of CydDC in a Native Lipid Bilayer Coupling Heme Transport to Antibiotic Resistance.
Journal, issue, pagesAdv Sci (Weinh), Page e76081, Year 2026
Publish dateJun 11, 2026
AuthorsLili Yang / Changbin Zhang / Mengyuan Lyu / Yongbo Luo / Jierou Zhang / Yujiao Chen / Lintao Luo / Wen Qiao / Xiangyangpeng Li / Yu Zhou / Zhongling Wei / Yuling Xiao / Qian Niu / Juan Zhou / Guanglin He / Binwu Ying / Zhaoming Su / Hao Chen / Xiaodi Tang / Haohao Dong /
PubMed AbstractHeme is an essential cofactor in numerous biological processes, including bacterial respiration. The ABC transporter CydDC facilitates the assembly and maturation of the cytochrome bd terminal ...Heme is an essential cofactor in numerous biological processes, including bacterial respiration. The ABC transporter CydDC facilitates the assembly and maturation of the cytochrome bd terminal oxidase by exporting heme and has been implicated in antibiotic resistance in bacteria. However, the dynamic conformations of CydDC in a native-like lipid bilayer remain unresolved, and its resistance mechanism is still elusive. Here, we determined high-resolution cryo-electron microscopy structures of nanodisc-reconstituted CydDC in the apo, nucleotide-bound and heme-bound states, providing direct structural evidence for its substrate-stimulated hydrolysis mechanism. In vivo and in vitro biochemical characterization identified key residues of CydDC that are critical for substrate binding and transport. Bioinformatics analysis further demonstrated that CydDC is highly conserved across bacterial species. Transcriptomic profiling of cydC/D in antibiotic-resistant strains showed that elevated expression of cydC/D correlates with increased antibiotic resistance. Moreover, mutations at the heme-binding sites altered bacterial susceptibility to multiple antibiotics, suggesting that the exporting activity of CydDC may also contribute directly to drug resistance. Together, these findings provide mechanistic insights into CydDC-mediated heme transport and potential drug efflux, and inform the development of antimicrobial strategies targeting the respiratory chain.
External linksAdv Sci (Weinh) / PubMed:42272423
MethodsEM (single particle)
Resolution2.82 - 3.71 Å
Structure data

55775

9tby

EMDB-55775, PDB-9tby:
apo state of CydDC in nanodisc
Method: EM (single particle) / Resolution: 3.71 Å

67054

9xno

EMDB-67054, PDB-9xno:
CydDC in nanodisc with AMP-PNP-bound
Method: EM (single particle) / Resolution: 2.93 Å

67055

9xnp

EMDB-67055, PDB-9xnp:
CydDC in nanodisc with ATP
Method: EM (single particle) / Resolution: 2.82 Å

67183

9xsm

EMDB-67183, PDB-9xsm:
CydDC in nanodisc with heme-bound I
Method: EM (single particle) / Resolution: 3.4 Å

67273

9xuo

EMDB-67273, PDB-9xuo:
CydDC in nanodisc with heme-bound II
Method: EM (single particle) / Resolution: 3.41 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

Source
  • escherichia coli k-12 (bacteria)
KeywordsTRANSPORT PROTEIN / nanodisc / AMP-PNP bound / ATP

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