Sandbox Reserved 1098: Difference between revisions

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==6HMM==

The <scene name='82/829351/6hmm/2'>6HMM protein</scene> is a human[[ poly (ADP-ribose) glycohydrolase]]. It is an enzyme that will catalyze the hydrolysis of glycosides, here more specifically it will produce a free ADP-ribose. This protein is only present when the DNA is damaged. It influences the damaged chromatin through a derepression on a gene promoter. Consequently this protein is quite interesting for biotechnological applications. Indeed, knowing the different pathways and protein interactions leading to DNA damage repair is a meaningful goal in research especially in new cancer therapies.

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This protein has four principal domains on a <scene name='82/829351/Single_chain/1'>single peptide chain</scene>: a A-domain, a catalytic domain and two substrate binding domains[http://www.uniprot.org/uniprot/Q86W56].

The first 456 amino acids of the peptide chain form the <scene name='82/829351/A_domain/1'>A-domain</scene>. Then from 610 to 795 amino acids is located the <scene name='82/829351/Catalytic_domain/1'>catalytic domain</scene>. This catalytic domain can binding with other proteins with <scene name='82/829351/Substrat_-_catalytic_domain/1'>two amino acids</scene> (the 726 and 727 amino acids). Next <scene name='82/829351/Subtrat_jonction_domain_2/1'>the second substrate binding domain</scene> is located from the 869 th to the 874th amino acids. [http://www.uniprot.org/uniprot/Q86W56]

So, most of the amino acids form the A-domain and the catzlytic domain and only few amino acids (8 a.a) make links with other proteins. Moreover, the ligand 7JB can bind the protein on the <scene name='82/829351/Liason_7jb/1'>754, 758, 792 and 795 amino acids</scene>. These amino acids are located on a helix and on a beta sheet. [~~https~~://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=6HMM]. So the amino acids of the protein is distributed like <scene name='82/829351/Distritbution_domain/1'>this</scene>.

So, most of the amino acids form the A-domain and the catzlytic domain and only few amino acids (8 a.a) make links with other proteins. Moreover, the ligand 7JB can bind the protein on the <scene name='82/829351/Liason_7jb/1'>754, 758, 792 and 795 amino acids</scene>. These amino acids are located on a helix and on a beta sheet. [http://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=6HMM]. So the amino acids of the protein is distributed like <scene name='82/829351/Distritbution_domain/1'>this</scene>.

=== Secondary Structure ===

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=== Tertiary Structure ===

The protein PARG folds into an ADP-ribose-binding macro domain with an N-terminal extension. It also consists of a diphosphate-binding loop

diphosphate-binding loop that flanks one side of the ADP-ribose binding cavity

opposite side of the PARG ADP-ribose binding cavity is lined by a stretch of amino acids corresponding to the PARG-specific GGG-X6–8-QEE signature sequence

PARG-specific loop is inserted into the macro domain fold to accommodate the Glu115 side chain that projects into the PARG active site (Fig. 3c, d). Due to the PARG-specific loop, it appears that only PARGs but not other macro domain proteins can hydrolyse PAR

=== Quaternary Structure ===

Poly(ADP-ribose)glycohydrolase interact with PCNA or NUDT5. When this protein is binding with NUDT5 it can remodeling chromatin.[http://www.uniprot.org/uniprot/Q86W56]

Poly(ADP-ribose)glycohydrolase interact with [[PCNA]] or [[NUDT5]]. When this protein is binding with NUDT5 it can remodeling chromatin.[http://www.uniprot.org/uniprot/Q86W56]

== Function ==

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@@ Line 2: / Line 2: @@
 ==6HMM==
 <StructureSection load='6hmm' size='340' side='right' caption='[[6hmm]]' scene=''>
 The <scene name='82/829351/6hmm/2'>6HMM protein</scene> is a human[[ poly (ADP-ribose) glycohydrolase]]. It is an enzyme that will catalyze the hydrolysis of glycosides, here more specifically it will produce a free ADP-ribose. This protein is only present when the DNA is damaged. It influences the damaged chromatin through a derepression on a gene promoter. Consequently this protein is quite interesting for biotechnological applications. Indeed, knowing the different pathways and protein interactions leading to DNA damage repair is a meaningful goal in research especially in new cancer therapies.
@@ Line 13: / Line 12: @@
 This protein has four principal domains on a <scene name='82/829351/Single_chain/1'>single peptide chain</scene>: a A-domain, a catalytic domain and two substrate binding domains[http://www.uniprot.org/uniprot/Q86W56].
 The first 456 amino acids of the peptide chain form the <scene name='82/829351/A_domain/1'>A-domain</scene>. Then from 610 to 795 amino acids is located the <scene name='82/829351/Catalytic_domain/1'>catalytic domain</scene>. This catalytic domain can binding with other proteins with <scene name='82/829351/Substrat_-_catalytic_domain/1'>two amino acids</scene> (the 726 and 727 amino acids). Next <scene name='82/829351/Subtrat_jonction_domain_2/1'>the second substrate binding domain</scene> is located from the 869 th to the 874th amino acids. [http://www.uniprot.org/uniprot/Q86W56]
-So, most of the amino acids form the A-domain and the catzlytic domain and only few amino acids (8 a.a) make links with other proteins. Moreover, the ligand 7JB can bind the protein on the <scene name='82/829351/Liason_7jb/1'>754, 758, 792 and 795 amino acids</scene>. These amino acids are located on a helix and on a beta sheet. [https://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=6HMM]. So the amino acids of the protein is distributed like <scene name='82/829351/Distritbution_domain/1'>this</scene>.
+So, most of the amino acids form the A-domain and the catzlytic domain and only few amino acids (8 a.a) make links with other proteins. Moreover, the ligand 7JB can bind the protein on the <scene name='82/829351/Liason_7jb/1'>754, 758, 792 and 795 amino acids</scene>. These amino acids are located on a helix and on a beta sheet. [http://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=6HMM]. So the amino acids of the protein is distributed like <scene name='82/829351/Distritbution_domain/1'>this</scene>.
 === Secondary Structure ===
@@ Line 22: / Line 21: @@
 === Tertiary Structure ===
+The protein PARG folds into an ADP-ribose-binding macro domain with an N-terminal extension. It also consists of a diphosphate-binding loop
+diphosphate-binding loop that flanks one side of the ADP-ribose binding cavity
+opposite side of the PARG ADP-ribose binding cavity is lined by a stretch of amino acids corresponding to the PARG-specific GGG-X6–8-QEE signature sequence
+PARG-specific loop is inserted into the macro domain fold to accommodate the Glu115 side chain that projects into the PARG active site (Fig. 3c, d). Due to the PARG-specific loop, it appears that only PARGs but not other macro domain proteins can hydrolyse PAR
+<ref>PMID: 21892188</ref>
 === Quaternary Structure ===
-Poly(ADP-ribose)glycohydrolase interact with PCNA or NUDT5. When this protein is binding with NUDT5 it can remodeling chromatin.[http://www.uniprot.org/uniprot/Q86W56]
+Poly(ADP-ribose)glycohydrolase interact with [[PCNA]] or [[NUDT5]]. When this protein is binding with NUDT5 it can remodeling chromatin.[http://www.uniprot.org/uniprot/Q86W56]
 == Function ==