Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Bacterial collagenase harnesses collagen geometry for processive cleavage.
Journal, issue, pages	Nat Commun, Year 2026
Publish date	Apr 2, 2026
Authors	Hiroya Oki / Katsuki Takebe / Adjoa Bonsu / Kazunori Fujii / Ryo Masuda / Nicholas Henderson / Takehiko Mima / Takaki Koide / Mahmoud Moradi / Osamu Matsushita / Joshua Sakon / Kazuki Kawahara /
PubMed Abstract	Collagen, the major structural protein in the animal extracellular matrix, forms a triple helix that resists proteolysis and requires specialised enzymes for degradation. Flesh-eating bacteria ...Collagen, the major structural protein in the animal extracellular matrix, forms a triple helix that resists proteolysis and requires specialised enzymes for degradation. Flesh-eating bacteria secrete collagenases that unwind the collagen triple helix and processively trim Gly-X-Y triplet repeats, yet the molecular basis of this process has remained obscure. Here, cryo-electron microscopy reveals how Hathewaya histolytica collagenase ColH engages its substrate and exploits the helix's architecture for catalysis. ColH encircles a single collagen triple helix in a closed-ring conformation and, through dynamic domain motions, dehydrates and destabilises it. The enzyme undergoes substrate-assisted twisting to adopt a rigid ratcheted conformation, in which one chain is bent into a tripeptide-long 'bight' and threaded into the active site for cleavage, while two uncut strands are partitioned to non-catalytic sites. Release of the bight appears to reset the enzyme, with the uncut strands serving as guiding tracks. Repeated cycling between dynamic and rigid states likely enables triplet-by-triplet translocation, allowing ColH to harness collagen's geometry for processive degradation. These findings reveal a bacterial strategy for collagen unwinding and cleavage distinct from that of mammalian collagenases, highlighting divergent evolutionary solutions for degrading one of nature's most intractable substrates.
External links	Nat Commun / PubMed:41927550
Methods	EM (single particle)
Resolution	2.2 - 3.41 Å
Structure data	63297 9lqj EMDB-63297: Cryo-EM map of collagenase H (E416Q mutant) from Hathewaya histolytica bound to C-terminal region of collagen model peptide (Pro-Hyp-Gly)10 PDB-9lqj: Cryo-EM structure of collagenase H (E416Q mutant) from Hathewaya histolytica bound to C-terminal region of collagen model peptide (Pro-Hyp-Gly)10 Method: EM (single particle) / Resolution: 2.68 Å EMDB-63331: Consensus map of apo collagenase H from Hathewaya histolytica Method: EM (single particle) / Resolution: 2.28 Å EMDB-63332: Cryo-EM map of apo collagenase H from Hathewaya histolytica - focused map of the Peptidase-Helper-PKD1 domains Method: EM (single particle) / Resolution: 2.24 Å EMDB-63333: Cryo-EM map of apo collagenase H from Hathewaya histolytica - focused map of the ARM domain Method: EM (single particle) / Resolution: 2.41 Å EMDB-63334: Consensus map of collagenase H (E416Q mutant) from Hathewaya histolytica in complex with collagen model peptide (Pro-Hyp-Gly)10 Method: EM (single particle) / Resolution: 3.33 Å EMDB-63335: Cryo-EM map of collagenase H (E416Q mutant) from Hathewaya histolytica in complex with collagen model peptide (Pro-Hyp-Gly)10 - focused map of ColH bound to the C-terminal region of collagen model peptide Method: EM (single particle) / Resolution: 3.06 Å EMDB-63336: Cryo-EM map of collagenase H (E416Q mutant) from Hathewaya histolytica in complex with collagen model peptide (Pro-Hyp-Gly)10 - focused map of ColH bound to the N-terminal region of collagen model peptide Method: EM (single particle) / Resolution: 3.41 Å 63337 9lrk EMDB-63337: Composite map of apo collagenase H from Hathewaya histolytica PDB-9lrk: Cryo-EM structure of apo collagenase H from Hathewaya histolytica Method: EM (single particle) / Resolution: 2.2 Å 63339 9lrm EMDB-63339: Composite map of collagenase H (E416Q mutant) from Hathewaya histolytica in complex with collagen model peptide (Pro-Hyp-Gly)10 PDB-9lrm: Cryo-EM structure of collagenase H (E416Q mutant) from Hathewaya histolytica in complex with collagen model peptide (Pro-Hyp-Gly)10 Method: EM (single particle) / Resolution: 3.4 Å EMDB-63508: Consensus map of collagenase H (E416Q mutant) from Hathewaya histolytica in complex with collagen model peptide (Pro-Hyp-Gly)12 Method: EM (single particle) / Resolution: 2.83 Å EMDB-63509: Cryo-EM map of collagenase H (E416Q mutant) from Hathewaya histolytica in complex with collagen model peptide (Pro-Hyp-Gly)12 - focused map of the ARM domain Method: EM (single particle) / Resolution: 2.86 Å EMDB-63510: Cryo-EM map of collagenase H (E416Q mutant) from Hathewaya histolytica in complex with collagen model peptide (Pro-Hyp-Gly)12 - focused map of the Peptidase-Helper-PKD1 domains Method: EM (single particle) / Resolution: 2.76 Å 63511 9lyi EMDB-63511: Composite map of collagenase H (E416Q mutant) from Hathewaya histolytica in complex with collagen model peptide (Pro-Hyp-Gly)12 PDB-9lyi: Cryo-EM structure of collagenase H (E416Q mutant) from Hathewaya histolytica in complex with collagen model peptide (Pro-Hyp-Gly)12 Method: EM (single particle) / Resolution: 2.8 Å 65889 9wdc EMDB-65889, PDB-9wdc: Cryo-EM structure of collagenase H (E416Q mutant) from Hathewaya histolytica bound to C-terminal region of the collagen-binding protein ColH (Pro-Pro-Gly)10 Method: EM (single particle) / Resolution: 2.22 Å
Chemicals	ChemComp-CA: Unknown entry ChemComp-ZN: Unknown entry ChemComp-HOH: WATER
Source	hathewaya histolytica (bacteria) homo sapiens (human)
Keywords	METAL BINDING PROTEIN / Collagenase / Hathewaya histolytica / Clostridium histolyticum