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Structures of three polycystic kidney disease-like domains from Clostridium histolyticum collagenases ColG and ColH.

Bauer R, Janowska K, Taylor K, Jordan B, Gann S, Janowski T, Latimer EC, Matsushita O, Sakon J - Acta Crystallogr. D Biol. Crystallogr. (2015)

Bottom Line: Surface aromatic residues found on ColH s2a-s2b, but not on ColG s2, may provide the weak interaction in the biphasic collagen-binding mode previously found in s2b-s3.Ca(2+) binding also increases stability against heat and guanidine hydrochloride, and may improve the longevity in the extracellular matrix.The results of this study will further assist in developing collagen-targeting vehicles for various signal molecules.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA.

ABSTRACT
Clostridium histolyticum collagenases ColG and ColH are segmental enzymes that are thought to be activated by Ca(2+)-triggered domain reorientation to cause extensive tissue destruction. The collagenases consist of a collagenase module (s1), a variable number of polycystic kidney disease-like (PKD-like) domains (s2a and s2b in ColH and s2 in ColG) and a variable number of collagen-binding domains (s3 in ColH and s3a and s3b in ColG). The X-ray crystal structures of Ca(2+)-bound holo s2b (1.4 Å resolution, R = 15.0%, Rfree = 19.1%) and holo s2a (1.9 Å resolution, R = 16.3%, Rfree = 20.7%), as well as of Ca(2+)-free apo s2a (1.8 Å resolution, R = 20.7%, Rfree = 27.2%) and two new forms of N-terminally truncated apo s2 (1.4 Å resolution, R = 16.9%, Rfree = 21.2%; 1.6 Å resolution, R = 16.2%, Rfree = 19.2%), are reported. The structurally similar PKD-like domains resemble the V-set Ig fold. In addition to a conserved β-bulge, the PKD-like domains feature a second bulge that also changes the allegiance of the subsequent β-strand. This β-bulge and the genesis of a Ca(2+) pocket in the archaeal PKD-like domain suggest a close kinship between bacterial and archaeal PKD-like domains. Different surface properties and indications of different dynamics suggest unique roles for the PKD-like domains in ColG and in ColH. Surface aromatic residues found on ColH s2a-s2b, but not on ColG s2, may provide the weak interaction in the biphasic collagen-binding mode previously found in s2b-s3. B-factor analyses suggest that in the presence of Ca(2+) the midsection of s2 becomes more flexible but the midsections of s2a and s2b stay rigid. The different surface properties and dynamics of the domains suggest that the PKD-like domains of M9B bacterial collagenase can be grouped into either a ColG subset or a ColH subset. The conserved properties of PKD-like domains in ColG and in ColH include Ca(2+) binding. Conserved residues not only interact with Ca(2+), but also position the Ca(2+)-interacting water molecule. Ca(2+) aligns the N-terminal linker approximately parallel to the major axis of the domain. Ca(2+) binding also increases stability against heat and guanidine hydrochloride, and may improve the longevity in the extracellular matrix. The results of this study will further assist in developing collagen-targeting vehicles for various signal molecules.

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Structural comparison of holo s2a (a), apo s2a (b), holo s2b (c) and apo s2 (d). Hydrogen bonds that stabilize β-bulges are highlighted. This figure was prepared using PyMOL (Schrödinger).
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fig2: Structural comparison of holo s2a (a), apo s2a (b), holo s2b (c) and apo s2 (d). Hydrogen bonds that stabilize β-bulges are highlighted. This figure was prepared using PyMOL (Schrödinger).

Mentions: In the following discussion, holo s2a will be described first (Fig. 2 ▶a). The eight holo s2a molecules are virtually identical (average r.m.s.d. of 0.2 ± 0.1 Å). Here, the molecules spiral along the crystallographic (1, 0, 1) axis. Along this axis, molecule pairs A and G, B and E, C and F, and D and H are related by NCS translation that results in an off-origin peak that is 63.9% of the origin peak in the Patterson map.


Structures of three polycystic kidney disease-like domains from Clostridium histolyticum collagenases ColG and ColH.

Bauer R, Janowska K, Taylor K, Jordan B, Gann S, Janowski T, Latimer EC, Matsushita O, Sakon J - Acta Crystallogr. D Biol. Crystallogr. (2015)

Structural comparison of holo s2a (a), apo s2a (b), holo s2b (c) and apo s2 (d). Hydrogen bonds that stabilize β-bulges are highlighted. This figure was prepared using PyMOL (Schrödinger).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4356367&req=5

fig2: Structural comparison of holo s2a (a), apo s2a (b), holo s2b (c) and apo s2 (d). Hydrogen bonds that stabilize β-bulges are highlighted. This figure was prepared using PyMOL (Schrödinger).
Mentions: In the following discussion, holo s2a will be described first (Fig. 2 ▶a). The eight holo s2a molecules are virtually identical (average r.m.s.d. of 0.2 ± 0.1 Å). Here, the molecules spiral along the crystallographic (1, 0, 1) axis. Along this axis, molecule pairs A and G, B and E, C and F, and D and H are related by NCS translation that results in an off-origin peak that is 63.9% of the origin peak in the Patterson map.

Bottom Line: Surface aromatic residues found on ColH s2a-s2b, but not on ColG s2, may provide the weak interaction in the biphasic collagen-binding mode previously found in s2b-s3.Ca(2+) binding also increases stability against heat and guanidine hydrochloride, and may improve the longevity in the extracellular matrix.The results of this study will further assist in developing collagen-targeting vehicles for various signal molecules.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA.

ABSTRACT
Clostridium histolyticum collagenases ColG and ColH are segmental enzymes that are thought to be activated by Ca(2+)-triggered domain reorientation to cause extensive tissue destruction. The collagenases consist of a collagenase module (s1), a variable number of polycystic kidney disease-like (PKD-like) domains (s2a and s2b in ColH and s2 in ColG) and a variable number of collagen-binding domains (s3 in ColH and s3a and s3b in ColG). The X-ray crystal structures of Ca(2+)-bound holo s2b (1.4 Å resolution, R = 15.0%, Rfree = 19.1%) and holo s2a (1.9 Å resolution, R = 16.3%, Rfree = 20.7%), as well as of Ca(2+)-free apo s2a (1.8 Å resolution, R = 20.7%, Rfree = 27.2%) and two new forms of N-terminally truncated apo s2 (1.4 Å resolution, R = 16.9%, Rfree = 21.2%; 1.6 Å resolution, R = 16.2%, Rfree = 19.2%), are reported. The structurally similar PKD-like domains resemble the V-set Ig fold. In addition to a conserved β-bulge, the PKD-like domains feature a second bulge that also changes the allegiance of the subsequent β-strand. This β-bulge and the genesis of a Ca(2+) pocket in the archaeal PKD-like domain suggest a close kinship between bacterial and archaeal PKD-like domains. Different surface properties and indications of different dynamics suggest unique roles for the PKD-like domains in ColG and in ColH. Surface aromatic residues found on ColH s2a-s2b, but not on ColG s2, may provide the weak interaction in the biphasic collagen-binding mode previously found in s2b-s3. B-factor analyses suggest that in the presence of Ca(2+) the midsection of s2 becomes more flexible but the midsections of s2a and s2b stay rigid. The different surface properties and dynamics of the domains suggest that the PKD-like domains of M9B bacterial collagenase can be grouped into either a ColG subset or a ColH subset. The conserved properties of PKD-like domains in ColG and in ColH include Ca(2+) binding. Conserved residues not only interact with Ca(2+), but also position the Ca(2+)-interacting water molecule. Ca(2+) aligns the N-terminal linker approximately parallel to the major axis of the domain. Ca(2+) binding also increases stability against heat and guanidine hydrochloride, and may improve the longevity in the extracellular matrix. The results of this study will further assist in developing collagen-targeting vehicles for various signal molecules.

Show MeSH
Related in: MedlinePlus