Sandbox Reserved 1125: Difference between revisions
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===== Zn998 : the structural zinc ===== | ===== Zn998 : the structural zinc ===== | ||
The residues involved in the Zn998 interactions are <scene name='71/719866/Zn998/2'>an Asp residue (149) next to three His residues (147, 162 and 175)</scene>. The glutamic acid adjacent to the first histidine is essential for catalysis. It should be noted that scientists were unable to exchange or remove this Zinc in their crystals, which is suggesting that there is a tight interaction with MMP-8.<ref name="X-ray"/> | The residues involved in the Zn998 interactions are <scene name='71/719866/Zn998/2'>an Asp residue (149) next to three His residues (147, 162 and 175)</scene>. The glutamic acid adjacent to the first histidine is essential for catalysis. It should be noted that scientists were unable to exchange or remove this Zinc in their crystals, which is suggesting that there is a tight interaction with MMP-8.<ref name="X-ray"/> | ||
==== Subsites ==== | ==== Subsites ==== | ||
Besides the catalytic site, the MMPs have other sites called subsites which can also interact with the substrates and inhibitors. Conventionally, the subsites on the left of the catalytic Zn2+ are designated as S1, S2, S3,..., Sn and the ones on the right are known as S1', S2', etc. | Besides the catalytic site, the MMPs have other sites called subsites which can also interact with the substrates and inhibitors. Conventionally, the subsites on the left of the catalytic Zn2+ are designated as S1, S2, S3,..., Sn and the ones on the right are known as S1', S2', etc. | ||
One of these subsites, the S1' pocket, is the main subsite for the substrate recognition. | One of these subsites, the S1' pocket, is the main subsite for the substrate recognition. This pocket is variable in amino acid composition and depth and can be used to classify the MMPs. | ||
MMP-8 belongs to the class of the intermediate MMPs according to the depth of its <scene name='71/719866/S1prime_pocket/1'>S1' pocket</scene>.<ref>PMID:22642189</ref> | MMP-8 belongs to the class of the intermediate MMPs according to the depth of its <scene name='71/719866/S1prime_pocket/1'>S1' pocket</scene>.<ref>PMID:22642189</ref> | ||
This pocket is delimited by the Leu193, Val194, His197, Leu214, Tyr216, Tyr219, Ala220 and Arg222 residues.<ref>PMID:17275314</ref>. | This pocket is delimited by the Leu193, Val194, His197, Leu214, Tyr216, Tyr219, Ala220 and Arg222 residues.<ref>PMID:17275314</ref>. | ||
Moreover this pocket is rich in hydrophobic amino acids, what is suitable for binding to the | Moreover this pocket is rich in hydrophobic amino acids, what is suitable for binding to the substrates of MMP-8. | ||
