Sandbox Reserved 468: Difference between revisions

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== Structure ==

The structure of MMP-1, just like the other members of matrix metalloproteinases family, is formed by different protein building blocks. The structure consists of a <scene name='Sandbox_Reserved_468/Catalytic_domain/2'>Catalytic Domain</scene>, a Linker Region and the <scene name='Sandbox_Reserved_468/Linker_region/1'>Hemopexin-like domain</scene>~~. The primary structure of MMP-1 was first published by Goldberg~~. Two main names for the primary structure are currently in use, the original one from which the first amino-acid starts with the signaling peptide and a second one where the first amino-acid starts counting from the prodomain (this is known as the proenzyme nomenclature).

The structure of MMP-1, just like the other members of matrix metalloproteinases family, is formed by different protein building blocks. The structure consists of a <scene name='Sandbox_Reserved_468/Catalytic_domain/2'>Catalytic Domain</scene>, a Linker Region and the <scene name='Sandbox_Reserved_468/Linker_region/1'>Hemopexin-like domain</scene>. Two main names for the primary structure are currently in use, the original one from which the first amino-acid starts with the signaling peptide and a second one where the first amino-acid starts counting from the prodomain (this is known as the proenzyme nomenclature).

'''Catalytic Domain'''

The Catalytic Domains of MMPs share very similar characteristics, having a general shape of oblate ellipsoid with a diameter of ~40Å. Despite the similarity of the Catalytic domains of MMPs, this entry will focus only on the structural features of MMP-1 Catalytic Domain.

The Catalytic Domains of all MMPs share very similar characteristics, having a general shape of oblate ellipsoid with a diameter of ~40Å. Despite the similarity of the Catalytic domains of MMPs, this entry will focus only on the structural features of MMP-1 Catalytic Domain. The <scene name='Sandbox_Reserved_468/Catalytic_domain/2'>Catalytic Domain</scene> of MMP-1 is composed of five highly twisted β-strands (sI-sV), three α-helix (hA-hC) and a total of eight loops, enclosing a total of five metal ions, three Ca2+ and two Zn2+, one of which with catalytic role.

The Catalytic Domain (CAT) of MMP-1 starts with the F100 as the first amino-acid of the N-terminal loop of the CAT domain. This is different from the first published x-ray structure of the CAT domain was showed the truncated form of this domain, where the first 7 amino-acids are not present.

'''Linker region'''

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'''Overall Structural Characteristics'''

The <scene name='Sandbox_Reserved_468/Catalytic_domain/2'>Catalytic Domain</scene> of MMP-1 is composed of five highly twisted β-strands (sI-sV), three α-helix (hA-hC) and a total of eight loops, enclosing a total of five metal ions, three Ca2+ and two Zn2+, one of which with catalytic role.

The Catalytic Domain (CAT) of MMP-1 starts with the F100 as the first amino-acid of the N-terminal loop of the CAT domain. This is different from the first published x-ray structure of the CAT domain was showed the truncated form of this domain, where the first 7 amino-acids are not present.

After the initial loop, the sequences follows to the first and longest β-sheet (sI). A second loop precedes large "amphipathic α-helix" (hA) that longitudinally spans protein site. The β-strands sII and sIII follows separated by the respective loops, loop 4 behing commonly designated as "short loop" briging sII to sIII. Following the sIII strand the sequence meets the 'S-shaped double loop' that is of primary importance for the peptide structure and catalytic activity ~~(see further)~~ as it extends to the cleft side "bulge", continuing to the only antiparallel β-strand sIV, which is prime importance for binding peptidic substrates or inhibitors by forming main chain Hydrogen bond. Following sIV, loop Gln186-Gly192 and β-strand sV are responsible for contributing with many ligands to the several metal ions present in the protein. A large open loop follows sV which has proven importance in substrate specificity within the MMPs family.

After the initial loop, the sequences follows to the first and longest β-sheet (sI). A second loop precedes large "amphipathic α-helix" (hA) that longitudinally spans protein site. The β-strands sII and sIII follows separated by the respective loops, loop 4 behing commonly designated as "short loop" briging sII to sIII. Following the sIII strand the sequence meets the 'S-shaped double loop' that is of primary importance for the peptide structure and catalytic activity as it extends to the cleft side "bulge", continuing to the only antiparallel β-strand sIV, which is prime importance for binding peptidic substrates or inhibitors by forming main chain Hydrogen bond. Following sIV, loop Gln186-Gly192 and β-strand sV are responsible for contributing with many ligands to the several metal ions present in the protein. A large open loop follows sV which has proven importance in substrate specificity within the MMPs family.

A specific region (183)RWTNNFREY(191) as been identified as a critical segment of matrix metalloproteinase 1 for the expression of collagenolytic activity. On C-terminal part of the CAT Domain the hB α-helix, known as the "active-site helix" encompasses part of the "zinc-binding consensus sequence" HEXXHXXGXXH that is characteristic of the Metzincin superfamily. The α-helix hB finishes abruptly at Gly225 where the last loop of the domain starts. This last loop contains the "specificity loop" which is the shortest in the MMPs family. The Catalytic Domain ends at Gly261 with α-helix hC.

Sandbox Reserved 468: Difference between revisions

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@@ Line 9: / Line 9: @@
 == Structure ==
-The structure of MMP-1, just like the other members of matrix metalloproteinases family, is formed by different protein building blocks. The structure consists of a <scene name='Sandbox_Reserved_468/Catalytic_domain/2'>Catalytic Domain</scene>, a Linker Region and the <scene name='Sandbox_Reserved_468/Linker_region/1'>Hemopexin-like domain</scene>. The primary structure of MMP-1 was first published by Goldberg. Two main names for the primary structure are currently in use, the original one from which the first amino-acid starts with the signaling peptide and a second one where the first amino-acid starts counting from the prodomain (this is known as the proenzyme nomenclature).
+The structure of MMP-1, just like the other members of matrix metalloproteinases family, is formed by different protein building blocks. The structure consists of a <scene name='Sandbox_Reserved_468/Catalytic_domain/2'>Catalytic Domain</scene>, a Linker Region and the <scene name='Sandbox_Reserved_468/Linker_region/1'>Hemopexin-like domain</scene>. Two main names for the primary structure are currently in use, the original one from which the first amino-acid starts with the signaling peptide and a second one where the first amino-acid starts counting from the prodomain (this is known as the proenzyme nomenclature).
 '''Catalytic Domain'''
-The Catalytic Domains of MMPs share very similar characteristics, having a general shape of oblate ellipsoid with a diameter of ~40Å. Despite the similarity of the Catalytic domains of MMPs, this entry will focus only on the structural features of MMP-1 Catalytic Domain.
+The Catalytic Domains of all MMPs share very similar characteristics, having a general shape of oblate ellipsoid with a diameter of ~40Å. Despite the similarity of the Catalytic domains of MMPs, this entry will focus only on the structural features of MMP-1 Catalytic Domain. The <scene name='Sandbox_Reserved_468/Catalytic_domain/2'>Catalytic Domain</scene> of MMP-1 is composed of five highly twisted β-strands (sI-sV), three α-helix (hA-hC) and a total of eight loops, enclosing a total of five metal ions, three Ca2+ and two Zn2+, one of which with catalytic role.
+The Catalytic Domain (CAT) of MMP-1 starts with the F100 as the first amino-acid of the N-terminal loop of the CAT domain. This is different from the first published x-ray structure of the CAT domain was showed the truncated form of this domain, where the first 7 amino-acids are not present.
 '''Linker region'''
@@ Line 26: / Line 27: @@
 '''Overall Structural Characteristics'''
-The <scene name='Sandbox_Reserved_468/Catalytic_domain/2'>Catalytic Domain</scene> of MMP-1 is composed of five highly twisted β-strands (sI-sV), three α-helix (hA-hC) and a total of eight loops, enclosing a total of five metal ions, three Ca2+ and two Zn2+, one of which with catalytic role.
-The Catalytic Domain (CAT) of MMP-1 starts with the F100 as the first amino-acid of the N-terminal loop of the CAT domain. This is different from the first published x-ray structure of the CAT domain was showed the truncated form of this domain, where the first 7 amino-acids are not present.
-After the initial loop, the sequences follows to the first and longest β-sheet (sI). A second loop precedes large "amphipathic α-helix" (hA) that longitudinally spans protein site. The β-strands sII and sIII follows separated by the respective loops, loop 4 behing commonly designated as "short loop" briging sII to sIII. Following the sIII strand the sequence meets the 'S-shaped double loop' that is of primary importance for the peptide structure and catalytic activity (see further) as it extends to the cleft side "bulge", continuing to the only antiparallel β-strand sIV, which is prime importance for binding peptidic substrates or inhibitors by forming main chain Hydrogen bond. Following sIV, loop Gln186-Gly192 and β-strand sV are responsible for contributing with many ligands to the several metal ions present in the protein. A large open loop follows sV which has proven importance in substrate specificity within the MMPs family.
+After the initial loop, the sequences follows to the first and longest β-sheet (sI). A second loop precedes large "amphipathic α-helix" (hA) that longitudinally spans protein site. The β-strands sII and sIII follows separated by the respective loops, loop 4 behing commonly designated as "short loop" briging sII to sIII. Following the sIII strand the sequence meets the 'S-shaped double loop' that is of primary importance for the peptide structure and catalytic activity as it extends to the cleft side "bulge", continuing to the only antiparallel β-strand sIV, which is prime importance for binding peptidic substrates or inhibitors by forming main chain Hydrogen bond. Following sIV, loop Gln186-Gly192 and β-strand sV are responsible for contributing with many ligands to the several metal ions present in the protein. A large open loop follows sV which has proven importance in substrate specificity within the MMPs family.
 A specific region (183)RWTNNFREY(191) as been identified as a critical segment of matrix metalloproteinase 1 for the expression of collagenolytic activity. On C-terminal part of the CAT Domain the hB α-helix, known as the "active-site helix" encompasses part of the "zinc-binding consensus sequence" HEXXHXXGXXH that is characteristic of the Metzincin superfamily. The α-helix hB finishes abruptly at Gly225 where the last loop of the domain starts. This last loop contains the "specificity loop" which is the shortest in the MMPs family. The Catalytic Domain ends at Gly261 with α-helix hC.