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3.4.24.3: microbial collagenase

This is an abbreviated version!
For detailed information about microbial collagenase, go to the full flat file.

Word Map on EC 3.4.24.3

Reaction

Digestion of native collagen in the triple helical region at -/-Gly bonds. With synthetic peptides, a preference is shown for Gly at P3 and P1', Pro and Ala at P2 and P2', and hydroxyproline, Ala or Arg at P3' =

Synonyms

120 kDa collagenase, Achromobacter iophagus collagenase, aspergillopeptidase C, azocollase, bacterial collagenase, bacterial collagenase V, BC_2466, CCA, ChC, class I collagenase, class II collagenase, class III collagenase, clostridial collagenase, clostridial collagenase A, clostridiopeptidase A, clostridiopeptidase I, clostridiopeptidase II, Clostridium histolyticum class II collagenase, Clostridium histolyticum collagenase, ColA, ColG, ColH, collagen peptidase, collagen protease, collagenase, collagenase A, collagenase clostridium histolyticum, collagenase G, collagenase H, collagenase I, collagenase MMP-1, collagenase T, ColT, Dupuytren clostridium histolyticum, Dupuytren collagenase, EC 3.4.24.8, EC 3.4.4.19, EC 3.4.99.5, kollaza, M9-peptidase, matirx metalloproteinase-18, matrix metalloproteinase-1, metallocollagenase, metalloproteinase ColB, metalloproteinase-1, microbial collagenase, MMP-1, More, nucleolysin, peptidase, clostridio-, A, proteinase, Clostridium histolyticum, A, soycollagestin, thermophilic collagenolytic protease, type I collagenase, type II collagenase, VMC peptidase

ECTree

     3 Hydrolases
         3.4 Acting on peptide bonds (peptidases)
             3.4.24 Metalloendopeptidases
                3.4.24.3 microbial collagenase

Crystallization

Crystallization on EC 3.4.24.3 - microbial collagenase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structures of the peptidase domains of ColT in the presence and absence of the peptidic inhibitor isoamylphosphonyl-Gly-Pro-Ala bound to the active site. Comparison of isoforms ColH, ColT and ColG reveals differences in domain breathing motions and regulatory elements. Calcium and zinc are required for full peptidolytic activity
apo-enzyme, free enzyme and in complex with inhibitor isoamyl-phosphonyl-Gly-Pro-Ala, to 2.55 A, 2.8 A and 3.25 A resolution. Structure shows a distinct segmentation of the N-terminal collagenase module, residues Tyr119-Gly790, forming a saddle-shaped two-domain architecture. The smaller N-terminal saddle flap serves as an activator domain, residues Tyr119-Asp388, and comprises an array of 12 parallel alpha-helices. The catalytic subdomain, residues Asp398-Gln669, adopts a thermolysin-like peptidase fold of mixed alpha and beta type. Leu517-Leu534 form the central helix of the fold and contain the Zn2+-binding 523-HEXXH-527 motif
crystal structure determination and analysis
crystal structure of ColG collagen-binding domain s3b, to 2.0 A resolution. All but one residue, whose side chain chelates with Ca2+, are conserved
crystal structures of ColH collagen-binding domain, to 2.0 A resolution. All but one residue, whose side chain chelates with Ca2+, are conserved. The dual Ca2+ binding site in s3 is completed by an unconserved aspartate. Domain s3 gains thermal stability, comparable to domain s3b of isoform ColG, by binding to Ca2+. holo s3 is also stabilized against chemical denaturants urea and guanidine HCl. The general shape of the binding pocket is retained by altered loop structures and side chain positions. Domain s3 also binds asymmetrically to minicollagen
crystal structures of the collagenase unit of ColG in the presence and absence of the peptidic inhibitor isoamylphosphonyl-Gly-Pro-Ala bound to the active site. Comparison of isoforms ColH, ColT and ColG reveals differences in domain breathing motions and regulatory elements. Calcium and zinc are required for full peptidolytic activity
crystal structures of the peptidase domains of ColH in the presence and absence of the peptidic inhibitor isoamylphosphonyl-Gly-Pro-Ala bound to the active site. In the unliganded ColH structure, the quaternary subdomain dynamics is modulated by an aspartate switch motion that binds to the catalytic zinc. One calcium binding site is in proximity to the catalytic zinc. Both ions are required for full activity. Loops close to the active site serve as characteristic substrate selectivity filter. Comparison of isoforms ColH, ColT and ColG reveals differences in domain breathing motions and regulatory elements. Calcium and zinc are required for full peptidolytic activity
hanging drop vapor diffusion method, structure of the collagen-binding domain with an N-terminal domain linker from class I collagenase, determined at 1.0 A resolution in the absence of Ca2+ and at 1.65 A resolution in the presence of calcium
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purified recombinant His-tagged catalytic domain of collagenase G, sitting drop vapour diffusion method, 10 mg/ml protein in 25 mM Tris, pH 7.5, and 50 mM NaCl, mixed with reservoir solution containing 0.12 M sodium citrate and 23% v/v PEG 3350 at 20°C, 10 days, X-ray diffraction structure determination and anaylsis at 2.75 A resolution
X-ray crystal structures of Ca2+-bound domain apo s2 to 1.4 A and 1.6 A resolution. ColG-derived domains lack surface aromatic residues, suggesting that the domain is less directly involved in interactions with collagen than that in isoform ColH. The domains are extremely stable in the presence of physiological concentrations of Ca2+
X-ray crystal structures of Ca2+-bound domains holo s2b to 1.4 A resolution, and holo s2a to 1.9 A resolution, as well as of Ca2+-free apo s2a to 1.8 A resolution. ColH-derived domains exhibit exposed aromatic residues and are found in M9B collagenases with a single collagen-binding domain. The domains are extremely stable in the presence of physiological concentrations of Ca2+