User:Abbas Raza/Sandbox 1 - Revision history

Abbas Raza at 12:33, 28 April 2014

Abbas Raza — Mon, 28 Apr 2014 12:33:08 GMT

←Older revision		Revision as of 12:33, 28 April 2014
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	Originally identified through in-silico studies from Wallace, Mitra and Seeger group back in 2002<ref>PMID: 12509226</ref>,<ref>PMID: 11904416</ref>,<ref>PMID: 12433996</ref> the crystallisation of NEIL3 remained challenge for almost a decade due to the difficulty in getting a stabilized form of the protein for crystallization until a truncated version was crystallized in 2013 <ref>PMID: 23313161</ref> and the crystal structure publlished as <scene name='58/583383/3w0f/2'>3W0F</scene>.		Originally identified through in-silico studies from Wallace, Mitra and Seeger group back in 2002<ref>PMID: 12509226</ref>,<ref>PMID: 11904416</ref>,<ref>PMID: 12433996</ref> the crystallisation of NEIL3 remained challenge for almost a decade due to the difficulty in getting a stabilized form of the protein for crystallization until a truncated version was crystallized in 2013 <ref>PMID: 23313161</ref> and the crystal structure publlished as <scene name='58/583383/3w0f/2'>3W0F</scene>.

-	NEIL3 proteins are almost twice the size of other Fpg/Nei family members (Figure 1C). This protein belongs to ~~alpha~~/~~beta~~[[http://en.wikipedia.org/wiki/Protein_fold_class]] category of proteins with the following secondary structure elements: <scene name='58/583383/3wof_3d_structure/24'>~~alpha~~-A(3-16)</scene>, <scene name='58/583383/3wof_3d_structure/27'>~~beta~~-1(23-27)</scene>, <scene name='58/583383/3wof_3d_structure/26'> ~~beta~~-2(73-79)</scene>, <scene name='58/583383/3wof_3d_structure/28'> ~~beta~~-3(82-87)</scene>, <scene name='58/583383/3wof_3d_structure/29'> ~~beta~~-4(90-96)</scene>, <scene name='58/583383/3wof_3d_structure/30'>~~beta~~-5(101-104)</scene>,<scene name='58/583383/3wof_3d_structure/31'>~~beta~~-6(119-123)</scene>,<scene name='58/583383/3wof_3d_structure/32'>~~beta~~-7(127-131)</scene>,<scene name='58/583383/3wof_3d_structure/33'>~~beta~~-8(133-139)</scene>,<scene name='58/583383/3wof_3d_structure/34'>~~alpha~~-B(140-150)</scene>, <scene name='58/583383/3wof_3d_structure/35'>~~alpha~~-C(162-171)</scene>, <scene name='58/583383/3wof_3d_structure/36'>~~alpha~~-D(177-182)</scene>,<scene name='58/583383/3wof_3d_structure/37'>~~alpha~~-E(192-202)</scene>,<scene name='58/583383/3wof_3d_structure/38'>~~alpha~~-F(215-238), </scene>,<scene name='58/583383/3wof_3d_structure/39'>~~beta~~-9(262-264)</scene>,	+	NEIL3 proteins are almost twice the size of other Fpg/Nei family members (Figure 1C). This protein belongs to α/β[[http://en.wikipedia.org/wiki/Protein_fold_class]] category of proteins with the following secondary structure elements: <scene name='58/583383/3wof_3d_structure/24'>α-A(3-16)</scene>, <scene name='58/583383/3wof_3d_structure/27'>β-1(23-27)</scene>, <scene name='58/583383/3wof_3d_structure/26'> β-2(73-79)</scene>, <scene name='58/583383/3wof_3d_structure/28'> β-3(82-87)</scene>, <scene name='58/583383/3wof_3d_structure/29'> β-4(90-96)</scene>, <scene name='58/583383/3wof_3d_structure/30'>β-5(101-104)</scene>,<scene name='58/583383/3wof_3d_structure/31'>β-6(119-123)</scene>,<scene name='58/583383/3wof_3d_structure/32'>β-7(127-131)</scene>,<scene name='58/583383/3wof_3d_structure/33'>β-8(133-139)</scene>,<scene name='58/583383/3wof_3d_structure/34'>α-B(140-150)</scene>, <scene name='58/583383/3wof_3d_structure/35'>α-C(162-171)</scene>, <scene name='58/583383/3wof_3d_structure/36'>α-D(177-182)</scene>,<scene name='58/583383/3wof_3d_structure/37'>α-E(192-202)</scene>,<scene name='58/583383/3wof_3d_structure/38'>α-F(215-238), </scene>,<scene name='58/583383/3wof_3d_structure/39'>β-9(262-264)</scene>,
-	<scene name='58/583383/3wof_3d_structure/40'>~~beta~~-10(273-275)</scene>. The beta strands form a two-layered <scene name='58/583383/Beta_strands/3'>beta sandwich</scene> at the N-terminus in which each layer is composed of four anti-parallel beta strands. The C terminus has a Helix 2 turn Helix (H2TH) motif formed by <scene name='58/583383/H2th/2'>~~alpha~~-C and D</scene> and a canonical	+	<scene name='58/583383/3wof_3d_structure/40'>β-10(273-275)</scene>. The beta strands form a two-layered <scene name='58/583383/Beta_strands/3'>beta sandwich</scene> at the N-terminus in which each layer is composed of four anti-parallel beta strands. The C terminus has a Helix 2 turn Helix (H2TH) motif formed by <scene name='58/583383/H2th/2'>α-C and α-D</scene> and a canonical
-	<scene name='58/583383/Zinc_finger/2'>zinc finger motif</scene> formed by the interconnecting loop between ~~beta~~ strands-9 and 10. In contrast to other Fpg/nei members, NEIL3 has two additional DNA binding domains at their C-terminus: one Ran binding protein (RanBP2)-type zinc finger motif and two identical GRF-zinc finger motif. The catalytic residue of MmuNEILL3 is a <scene name='58/583383/3wof_3d_structure/41'>~~Val-2~~</scene> rather than a proline as for other Fpg/nei members but serves the same purpose in catalysis and is surrounded by <scene name='58/583383/3wof_3d_structure/42'>~~R272~~, ~~Y250~~ C247, ~~F233~~,~~I-194~~ and ~~M99~~</scene> that forms the DNA binding cleft and lesion binding pocket of NEIL3.	+	<scene name='58/583383/Zinc_finger/2'>zinc finger motif</scene> formed by the interconnecting loop between β strands-9 and 10. In contrast to other Fpg/nei members, NEIL3 has two additional DNA binding domains at their C-terminus: one Ran binding protein (RanBP2)-type zinc finger motif and two identical GRF-zinc finger motif but they were not available in the truncated [[3w0f]] model. The catalytic residue of MmuNEILL3 is a <scene name='58/583383/3wof_3d_structure/41'>Val2</scene> rather than a proline as for other Fpg/nei members but serves the same purpose in catalysis and is surrounded by <scene name='58/583383/3wof_3d_structure/42'>Arg272, Tyr250 C247, Phe233,Ile194 and Met99</scene> that forms the DNA binding cleft and lesion binding pocket of NEIL3.


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	== '''Biological Function''' ==		== '''Biological Function''' ==

-	MmuNeil3 is a bifunctional DNA glycosylase that exhibits a broad substrate recognition spectrum (Sp, Gh, Fa pyG, FapyA, MeFapyG, DHU, DHT, 5-OHU, 5-OHC,5-OHMH, Tg, 8-oxoA, AP) but not 8-oxo-G (Figure2). [[Image:Dna_lesions.png\|thumb\|left\|300px\|'''Figure 2. DNA damages repaired by NEIL3''']]. The reason being that ~~alpha~~-B in Neil3 does not align with the corresponding helix in the other Nei families (Figure 2). Additional stabilizing bonds by residues Asp-155, Ile-156, and Ser-158 and neighboring residues Gly-81 and Arg-227 create a restricted movement and hence catalysis of predominately single stranded lesions by MmNEIL3 (Figure3)[[Image:Alignment_neils.png\|thumb\|left\|300px\| '''Figure 3. Alignment of the alpha-B-alpha-C helices from different NEIL enzymes.''' Analysis of the ~~alpha~~-B-~~alpha~~-C from MmuNeil3 with that of NEIL1 (residues 126–151) and bacteriial nei (residue 113–145) confirms why 8-oxo-G cannot be recognized easily]].	+	MmuNeil3 is a bifunctional DNA glycosylase that exhibits a broad substrate recognition spectrum (Sp, Gh, Fa pyG, FapyA, MeFapyG, DHU, DHT, 5-OHU, 5-OHC,5-OHMH, Tg, 8-oxoA, AP) but not 8-oxo-G (Figure2). [[Image:Dna_lesions.png\|thumb\|left\|300px\|'''Figure 2. DNA damages repaired by NEIL3''']]. The reason being that α-B in Neil3 does not align with the corresponding helix in the other Nei families (Figure 2). Additional stabilizing bonds by residues Asp-155, Ile-156, and Ser-158 and neighboring residues Gly-81 and Arg-227 create a restricted movement and hence catalysis of predominately '''single stranded lesions''' by MmNEIL3 (Figure3)[[Image:Alignment_neils.png\|thumb\|left\|300px\| '''Figure 3. Alignment of the alpha-B-alpha-C helices from different NEIL enzymes.''' Analysis of the α-B-α-C from MmuNeil3 with that of NEIL1 (residues 126–151) and bacteriial nei (residue 113–145) confirms why 8-oxo-G cannot be recognized easily]].
	The DNA structures attacked most often are large bubble and single stranded DNA and least duplex DNA<ref>PMID: 23274422</ref>. NEIL2 is similar to NEIL3 in terms of substrates attacked whereas NEIL1 on the other hand, prefers double stranded DNA lesions. The idea of having multiple enzymes to repair the same lesion confirms that NEIL3 might act as a backup line of defense against oxidative damage.		The DNA structures attacked most often are large bubble and single stranded DNA and least duplex DNA<ref>PMID: 23274422</ref>. NEIL2 is similar to NEIL3 in terms of substrates attacked whereas NEIL1 on the other hand, prefers double stranded DNA lesions. The idea of having multiple enzymes to repair the same lesion confirms that NEIL3 might act as a backup line of defense against oxidative damage.

Abbas Raza at 12:23, 28 April 2014

Abbas Raza — Mon, 28 Apr 2014 12:23:52 GMT

←Older revision		Revision as of 12:23, 28 April 2014
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	== '''Biological Function''' ==		== '''Biological Function''' ==

-	MmuNeil3 is a bifunctional DNA glycosylase that exhibits a broad substrate recognition spectrum (Sp, Gh, Fa pyG, FapyA, MeFapyG, DHU, DHT, 5-OHU, 5-OHC,5-OHMH, Tg, 8-oxoA, AP) but not 8-oxo-G. The reason being that alpha-B in Neil3 does not align with the corresponding helix in the other Nei families (Figure 2). Additional stabilizing bonds by residues Asp-155, Ile-156, and Ser-158 and neighboring residues Gly-81 and Arg-227 create a restricted movement and hence catalysis of predominately single stranded lesions by MmNEIL3.	+	MmuNeil3 is a bifunctional DNA glycosylase that exhibits a broad substrate recognition spectrum (Sp, Gh, Fa pyG, FapyA, MeFapyG, DHU, DHT, 5-OHU, 5-OHC,5-OHMH, Tg, 8-oxoA, AP) but not 8-oxo-G (Figure2). [[Image:Dna_lesions.png\|thumb\|left\|300px\|'''Figure 2. DNA damages repaired by NEIL3''']]. The reason being that alpha-B in Neil3 does not align with the corresponding helix in the other Nei families (Figure 2). Additional stabilizing bonds by residues Asp-155, Ile-156, and Ser-158 and neighboring residues Gly-81 and Arg-227 create a restricted movement and hence catalysis of predominately single stranded lesions by MmNEIL3 (Figure3)[[Image:Alignment_neils.png\|thumb\|left\|300px\| '''Figure 3. Alignment of the alpha-B-alpha-C helices from different NEIL enzymes.''' Analysis of the alpha-B-alpha-C from MmuNeil3 with that of NEIL1 (residues 126–151) and bacteriial nei (residue 113–145) confirms why 8-oxo-G cannot be recognized easily]].
-	[[Image:Alignment_neils.png\|thumb\|left\|300px\| '''Figure 2. Alignment of the alpha-B-alpha-C helices from different NEIL enzymes.''' Analysis of the alpha-B-alpha-C from MmuNeil3 with that of NEIL1 (residues 126–151) and bacteriial nei (residue 113–145) confirms why 8-oxo-G cannot be recognized easily]].	+
	The DNA structures attacked most often are large bubble and single stranded DNA and least duplex DNA<ref>PMID: 23274422</ref>. NEIL2 is similar to NEIL3 in terms of substrates attacked whereas NEIL1 on the other hand, prefers double stranded DNA lesions. The idea of having multiple enzymes to repair the same lesion confirms that NEIL3 might act as a backup line of defense against oxidative damage.		The DNA structures attacked most often are large bubble and single stranded DNA and least duplex DNA<ref>PMID: 23274422</ref>. NEIL2 is similar to NEIL3 in terms of substrates attacked whereas NEIL1 on the other hand, prefers double stranded DNA lesions. The idea of having multiple enzymes to repair the same lesion confirms that NEIL3 might act as a backup line of defense against oxidative damage.
-	~~[[Image:Dna_lesions.png\|thumb\|left\|300px\|'''Figure 3. DNA damages repaired by NEIL3''']]~~	+

	== NEIL3 expression and localisation ==		== NEIL3 expression and localisation ==

Abbas Raza at 12:04, 28 April 2014

Abbas Raza — Mon, 28 Apr 2014 12:04:18 GMT

←Older revision		Revision as of 12:04, 28 April 2014
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	=='''3D structures of other Fpg/nei members'''==		=='''3D structures of other Fpg/nei members'''==
		+	Updated on {{REVISIONDAY2}}-{{MONTHNAME\|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}

	=== NEIL1 ===		=== NEIL1 ===

Abbas Raza at 11:58, 28 April 2014

Abbas Raza — Mon, 28 Apr 2014 11:58:48 GMT

←Older revision		Revision as of 11:58, 28 April 2014
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	=== NEIL1 ===		=== NEIL1 ===

-	[[1tdh]] [[3a42]],[[3a45]], [[3a46]], [[3vk7]], [[3vk8]], [[4nrv]], [[4nrw]]	+	[[1tdh]], [[3a42]], [[3a45]], [[3a46]], [[3vk7]], [[3vk8]], [[4nrv]], [[4nrw]]

	=== NEIL2 ===		=== NEIL2 ===
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	MmuNeil3 is a bifunctional DNA glycosylase that exhibits a broad substrate recognition spectrum (Sp, Gh, Fa pyG, FapyA, MeFapyG, DHU, DHT, 5-OHU, 5-OHC,5-OHMH, Tg, 8-oxoA, AP) but not 8-oxo-G. The reason being that alpha-B in Neil3 does not align with the corresponding helix in the other Nei families (Figure 2). Additional stabilizing bonds by residues Asp-155, Ile-156, and Ser-158 and neighboring residues Gly-81 and Arg-227 create a restricted movement and hence catalysis of predominately single stranded lesions by MmNEIL3.		MmuNeil3 is a bifunctional DNA glycosylase that exhibits a broad substrate recognition spectrum (Sp, Gh, Fa pyG, FapyA, MeFapyG, DHU, DHT, 5-OHU, 5-OHC,5-OHMH, Tg, 8-oxoA, AP) but not 8-oxo-G. The reason being that alpha-B in Neil3 does not align with the corresponding helix in the other Nei families (Figure 2). Additional stabilizing bonds by residues Asp-155, Ile-156, and Ser-158 and neighboring residues Gly-81 and Arg-227 create a restricted movement and hence catalysis of predominately single stranded lesions by MmNEIL3.
-	[[Image:Alignment_neils.png\|thumb\|left\|300px\| '''Figure 2. Alignment of the alpha-B-alpha-C.''' Analysis of the alpha-B-alpha-C from MmuNeil3 with that of NEIL1 (residues 126–151) and bacteriial nei (residue 113–145)]].	+	[[Image:Alignment_neils.png\|thumb\|left\|300px\| '''Figure 2. Alignment of the alpha-B-alpha-C helices from different NEIL enzymes.''' Analysis of the alpha-B-alpha-C from MmuNeil3 with that of NEIL1 (residues 126–151) and bacteriial nei (residue 113–145) confirms why 8-oxo-G cannot be recognized easily]].
	The DNA structures attacked most often are large bubble and single stranded DNA and least duplex DNA<ref>PMID: 23274422</ref>. NEIL2 is similar to NEIL3 in terms of substrates attacked whereas NEIL1 on the other hand, prefers double stranded DNA lesions. The idea of having multiple enzymes to repair the same lesion confirms that NEIL3 might act as a backup line of defense against oxidative damage.		The DNA structures attacked most often are large bubble and single stranded DNA and least duplex DNA<ref>PMID: 23274422</ref>. NEIL2 is similar to NEIL3 in terms of substrates attacked whereas NEIL1 on the other hand, prefers double stranded DNA lesions. The idea of having multiple enzymes to repair the same lesion confirms that NEIL3 might act as a backup line of defense against oxidative damage.
	[[Image:Dna_lesions.png\|thumb\|left\|300px\|'''Figure 3. DNA damages repaired by NEIL3''']]		[[Image:Dna_lesions.png\|thumb\|left\|300px\|'''Figure 3. DNA damages repaired by NEIL3''']]

Abbas Raza at 11:54, 28 April 2014

Abbas Raza — Mon, 28 Apr 2014 11:54:39 GMT

←Older revision		Revision as of 11:54, 28 April 2014
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	[[Image:NEIL3 domains.png\|thumb\|left\|300px\|'''Figure 1. Mouse NEIL3''' (A) Cartoon representation of NEIL3 domains (pdb id 3w0f) (B) full length MmNEIL3 protein showing additional DNA binding domains (RANbp and GRF) not found in other neil/fpg proteins and (C)Comparison of NEIL3 proteins with other fpg/neil members, the color coding follows the same domains as in (B)]]		[[Image:NEIL3 domains.png\|thumb\|left\|300px\|'''Figure 1. Mouse NEIL3''' (A) Cartoon representation of NEIL3 domains (pdb id 3w0f) (B) full length MmNEIL3 protein showing additional DNA binding domains (RANbp and GRF) not found in other neil/fpg proteins and (C)Comparison of NEIL3 proteins with other fpg/neil members, the color coding follows the same domains as in (B)]]

-	This protein is a unique member of DNA glysosylases, family of base excision repair enzymes that show preference for both oxidative purines and pyrimidine lesions. For a description of all known DNA glycosylases and their families see the wikepedia page on DNA glycosylases [[http://en.wikipedia.org/wiki/DNA_glycosylase]]. Originally identified through in-silico studies from Wallace, Mitra and Seeger group back in 2002<ref>PMID: 12509226</ref>,<ref>PMID: 11904416</ref>,<ref>PMID: 12433996</ref> the crystallisation of NEIL3 remained challenge for almost a decade due to the difficulty in getting a stabilized form of the protein for crystallization until a truncated version was crystallized in 2013 <ref>PMID: 23313161</ref> and the crystal structure publlished as <scene name='58/583383/3w0f/2'>3W0F</scene>.	+	This protein is a unique member of DNA glysosylases, family of base excision repair enzymes that show preference for both oxidative purines and pyrimidine lesions. For a description of all known DNA glycosylases and their families see the wikepedia page on DNA glycosylases [[http://en.wikipedia.org/wiki/DNA_glycosylase]]. There is also a separate proteopedia page on Nei/fpg family [[http://proteopedia.org/wiki/index.php/Fpg_Nei_Protein_Family]].
		+
		+	Originally identified through in-silico studies from Wallace, Mitra and Seeger group back in 2002<ref>PMID: 12509226</ref>,<ref>PMID: 11904416</ref>,<ref>PMID: 12433996</ref> the crystallisation of NEIL3 remained challenge for almost a decade due to the difficulty in getting a stabilized form of the protein for crystallization until a truncated version was crystallized in 2013 <ref>PMID: 23313161</ref> and the crystal structure publlished as <scene name='58/583383/3w0f/2'>3W0F</scene>.

	NEIL3 proteins are almost twice the size of other Fpg/Nei family members (Figure 1C). This protein belongs to alpha/beta[[http://en.wikipedia.org/wiki/Protein_fold_class]] category of proteins with the following secondary structure elements: <scene name='58/583383/3wof_3d_structure/24'>alpha-A(3-16)</scene>, <scene name='58/583383/3wof_3d_structure/27'>beta-1(23-27)</scene>, <scene name='58/583383/3wof_3d_structure/26'> beta-2(73-79)</scene>, <scene name='58/583383/3wof_3d_structure/28'> beta-3(82-87)</scene>, <scene name='58/583383/3wof_3d_structure/29'> beta-4(90-96)</scene>, <scene name='58/583383/3wof_3d_structure/30'>beta-5(101-104)</scene>,<scene name='58/583383/3wof_3d_structure/31'>beta-6(119-123)</scene>,<scene name='58/583383/3wof_3d_structure/32'>beta-7(127-131)</scene>,<scene name='58/583383/3wof_3d_structure/33'>beta-8(133-139)</scene>,<scene name='58/583383/3wof_3d_structure/34'>alpha-B(140-150)</scene>, <scene name='58/583383/3wof_3d_structure/35'>alpha-C(162-171)</scene>, <scene name='58/583383/3wof_3d_structure/36'>alpha-D(177-182)</scene>,<scene name='58/583383/3wof_3d_structure/37'>alpha-E(192-202)</scene>,<scene name='58/583383/3wof_3d_structure/38'>alpha-F(215-238), </scene>,<scene name='58/583383/3wof_3d_structure/39'>beta-9(262-264)</scene>,		NEIL3 proteins are almost twice the size of other Fpg/Nei family members (Figure 1C). This protein belongs to alpha/beta[[http://en.wikipedia.org/wiki/Protein_fold_class]] category of proteins with the following secondary structure elements: <scene name='58/583383/3wof_3d_structure/24'>alpha-A(3-16)</scene>, <scene name='58/583383/3wof_3d_structure/27'>beta-1(23-27)</scene>, <scene name='58/583383/3wof_3d_structure/26'> beta-2(73-79)</scene>, <scene name='58/583383/3wof_3d_structure/28'> beta-3(82-87)</scene>, <scene name='58/583383/3wof_3d_structure/29'> beta-4(90-96)</scene>, <scene name='58/583383/3wof_3d_structure/30'>beta-5(101-104)</scene>,<scene name='58/583383/3wof_3d_structure/31'>beta-6(119-123)</scene>,<scene name='58/583383/3wof_3d_structure/32'>beta-7(127-131)</scene>,<scene name='58/583383/3wof_3d_structure/33'>beta-8(133-139)</scene>,<scene name='58/583383/3wof_3d_structure/34'>alpha-B(140-150)</scene>, <scene name='58/583383/3wof_3d_structure/35'>alpha-C(162-171)</scene>, <scene name='58/583383/3wof_3d_structure/36'>alpha-D(177-182)</scene>,<scene name='58/583383/3wof_3d_structure/37'>alpha-E(192-202)</scene>,<scene name='58/583383/3wof_3d_structure/38'>alpha-F(215-238), </scene>,<scene name='58/583383/3wof_3d_structure/39'>beta-9(262-264)</scene>,

Abbas Raza at 11:47, 28 April 2014

Abbas Raza — Mon, 28 Apr 2014 11:47:42 GMT

←Older revision		Revision as of 11:47, 28 April 2014
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	=== Fpg ===		=== Fpg ===

-	[[3twk]], [[3twl]], [[3twm]], [[1pjj]], [[1r2y]], [[1ee8]], [[1k82]], [[1l1z]], [[1l2b]], [[1l2c]], [[1l1t], [[1l2d]], [[1r2z]], [[1pm5]], [[1nnj]], [[1kfv]], [[1pji]], [[3c58]], [[3vk5]], [[2xzu]], [[2xzf]], [[1tdz]], [[1xc8]]	+	[[3twk]], [[3twl]], [[3twm]], [[1pjj]], [[1r2y]], [[1ee8]], [[1k82]], [[1l1z]], [[1l2b]], [[1l2c]], [[1l1t]], [[1l2d]], [[1r2z]], [[1pm5]], [[1nnj]], [[1kfv]], [[1pji]], [[3c58]], [[3vk5]], [[2xzu]], [[2xzf]], [[1tdz]], [[1xc8]]

	=== Nei ===		=== Nei ===

Abbas Raza at 11:45, 28 April 2014

Abbas Raza — Mon, 28 Apr 2014 11:45:24 GMT

←Older revision		Revision as of 11:45, 28 April 2014
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	=== NEIL1 ===		=== NEIL1 ===

-	[[1tdh]] [[3a42]],[[3a45]], [[3a46]],[[3vk7]], [[3vk8]], [[4nrv]], [[4nrw]]	+	[[1tdh]] [[3a42]],[[3a45]], [[3a46]], [[3vk7]], [[3vk8]], [[4nrv]], [[4nrw]]

	=== NEIL2 ===		=== NEIL2 ===

Abbas Raza at 11:44, 28 April 2014

Abbas Raza — Mon, 28 Apr 2014 11:44:15 GMT

←Older revision		Revision as of 11:44, 28 April 2014
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	=== NEIL1 ===		=== NEIL1 ===

-	[[1tdh]] [[3a42]],[[~~3A45~~]], [[~~3A46~~]],[[~~3VK7~~]], [[~~3VK8~~]], [[~~4NRV~~]], [[~~4NRW~~]]	+	[[1tdh]] [[3a42]],[[3a45]], [[3a46]],[[3vk7]], [[3vk8]], [[4nrv]], [[4nrw]]

	=== NEIL2 ===		=== NEIL2 ===

-	[[~~4MB7~~]]	+	[[4mb7]]

	=== Fpg ===		=== Fpg ===

-	[[3twk]], [[3twl]], [[3twm]], [[1pjj]], [[1r2y]], [[1ee8]], [[1k82]], [[~~1L1Z~~]], [[~~1L2B~~]], [[~~1L2C~~]], [[~~1L1T~~], [[~~1L2D~~]], [[~~1R2Z~~]], [[~~1PM5~~]], [[~~1NNJ~~]], [[~~1KFV~~]], [[~~1PJI~~]], [[~~3C58~~]], [[~~3VK5~~]], [[~~2XZU~~]], [[~~2XZF~~]], [[~~1TDZ~~]], [[~~1XC8~~]]	+	[[3twk]], [[3twl]], [[3twm]], [[1pjj]], [[1r2y]], [[1ee8]], [[1k82]], [[1l1z]], [[1l2b]], [[1l2c]], [[1l1t], [[1l2d]], [[1r2z]], [[1pm5]], [[1nnj]], [[1kfv]], [[1pji]], [[3c58]], [[3vk5]], [[2xzu]], [[2xzf]], [[1tdz]], [[1xc8]]

	=== Nei ===		=== Nei ===

-	[[~~2EA0~~]], [[~~2OPF~~]], [[~~2OQ4~~]], [[~~1Q3C~~]], [[~~1Q3B~~]], [[~~1Q39~~]]	+	[[2eao]], [[2opf]], [[2oq4]], [[1q3c]], [[1q3b]], [[1q39]]

Abbas Raza at 11:39, 28 April 2014

Abbas Raza — Mon, 28 Apr 2014 11:39:33 GMT

←Older revision		Revision as of 11:39, 28 April 2014
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	<scene name='58/583383/3wof_3d_structure/40'>beta-10(273-275)</scene>. The beta strands form a two-layered <scene name='58/583383/Beta_strands/3'>beta sandwich</scene> at the N-terminus in which each layer is composed of four anti-parallel beta strands. The C terminus has a Helix 2 turn Helix (H2TH) motif formed by <scene name='58/583383/H2th/2'>alpha-C and D</scene> and a canonical		<scene name='58/583383/3wof_3d_structure/40'>beta-10(273-275)</scene>. The beta strands form a two-layered <scene name='58/583383/Beta_strands/3'>beta sandwich</scene> at the N-terminus in which each layer is composed of four anti-parallel beta strands. The C terminus has a Helix 2 turn Helix (H2TH) motif formed by <scene name='58/583383/H2th/2'>alpha-C and D</scene> and a canonical
	<scene name='58/583383/Zinc_finger/2'>zinc finger motif</scene> formed by the interconnecting loop between beta strands-9 and 10. In contrast to other Fpg/nei members, NEIL3 has two additional DNA binding domains at their C-terminus: one Ran binding protein (RanBP2)-type zinc finger motif and two identical GRF-zinc finger motif. The catalytic residue of MmuNEILL3 is a <scene name='58/583383/3wof_3d_structure/41'>Val-2</scene> rather than a proline as for other Fpg/nei members but serves the same purpose in catalysis and is surrounded by <scene name='58/583383/3wof_3d_structure/42'>R272, Y250 C247, F233,I-194 and M99</scene> that forms the DNA binding cleft and lesion binding pocket of NEIL3.		<scene name='58/583383/Zinc_finger/2'>zinc finger motif</scene> formed by the interconnecting loop between beta strands-9 and 10. In contrast to other Fpg/nei members, NEIL3 has two additional DNA binding domains at their C-terminus: one Ran binding protein (RanBP2)-type zinc finger motif and two identical GRF-zinc finger motif. The catalytic residue of MmuNEILL3 is a <scene name='58/583383/3wof_3d_structure/41'>Val-2</scene> rather than a proline as for other Fpg/nei members but serves the same purpose in catalysis and is surrounded by <scene name='58/583383/3wof_3d_structure/42'>R272, Y250 C247, F233,I-194 and M99</scene> that forms the DNA binding cleft and lesion binding pocket of NEIL3.
		+
		+
		+	----
		+
		+	=='''3D structures of other Fpg/nei members'''==
		+
		+	=== NEIL1 ===
		+
		+	[[1tdh]] [[3a42]],[[3A45]], [[3A46]],[[3VK7]], [[3VK8]], [[4NRV]], [[4NRW]]
		+
		+	=== NEIL2 ===
		+
		+	[[4MB7]]
		+
		+	=== Fpg ===
		+
		+	[[3twk]], [[3twl]], [[3twm]], [[1pjj]], [[1r2y]], [[1ee8]], [[1k82]], [[1L1Z]], [[1L2B]], [[1L2C]], [[1L1T], [[1L2D]], [[1R2Z]], [[1PM5]], [[1NNJ]], [[1KFV]], [[1PJI]], [[3C58]], [[3VK5]], [[2XZU]], [[2XZF]], [[1TDZ]], [[1XC8]]
		+
		+	=== Nei ===
		+
		+	[[2EA0]], [[2OPF]], [[2OQ4]], [[1Q3C]], [[1Q3B]], [[1Q39]]

Abbas Raza at 23:01, 27 April 2014

Abbas Raza — Sun, 27 Apr 2014 23:01:33 GMT

←Older revision		Revision as of 23:01, 27 April 2014
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	== Disease ==		== Disease ==
	Experiments with knock-out NEIL3-/-mice showed that the animals were viable and fertile and had no obvious contrasting phenotype<ref>PMID: 16428305</ref> . However, later studies have reported memory defects and reduced anxiety like symptoms in C57BL/6 mice indicative of impaired proliferatived neural cells but no defects in fertility or viability<ref>PMID: 22065741</ref>. This adds to the idea that the biological function of NEIL3 is not exclusively restricted to DNA repair. High expression in spleen and bone marrow hints a role in immune system.		Experiments with knock-out NEIL3-/-mice showed that the animals were viable and fertile and had no obvious contrasting phenotype<ref>PMID: 16428305</ref> . However, later studies have reported memory defects and reduced anxiety like symptoms in C57BL/6 mice indicative of impaired proliferatived neural cells but no defects in fertility or viability<ref>PMID: 22065741</ref>. This adds to the idea that the biological function of NEIL3 is not exclusively restricted to DNA repair. High expression in spleen and bone marrow hints a role in immune system.
-	== Relevance ==

-	== Structural highlights ==

-	This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
-
-	</StructureSection>
	== References ==		== References ==
	<references/>		<references/>