1pc8: Difference between revisions

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~~[[Image:1pc8.gif|left|200px]]<br /><applet load="1pc8" size="450" color="white" frame="true" align="right" spinBox="true"~~

~~caption="1pc8, resolution 3.80Å" />~~

~~'''Crystal Structure of a novel form of mistletoe lectin from Himalayan Viscum album L. at 3.8A resolution'''<br />~~

==~~Overview~~==

==Crystal Structure of a novel form of mistletoe lectin from Himalayan Viscum album L. at 3.8A resolution==

This is the first report of the structural studies of a novel, ribosome-inactivating protein (RIP) obtained from the Himalayan mistletoe, (Viscum album) (HmRip). HmRip is a type II heterodimeric protein, consisting of a toxic enzyme (A-chain) with an active site for ribosome, inactivation and a lectin subunit (B-chain) with well defined, sugar-binding sites. The crystal structure of HmRip has been determined at, 3.8 A resolution and refined to a crystallographic R factor of 0.228, (R(free) = 0.271). A comparison of this structure with other type II RIPs, reveals the presence of distinct structural features in the active site of, the A-chain and in the 2gamma sugar-binding site of the B-chain. The, conformation of the side chain of Tyr110, which is a conserved active-site, residue in the A subunit, is strikingly different from those observed in, other mistletoe RIPs, indicating its unique substrate-binding preference., The deletion of two important residues from the kink region after Ala231, in the 2gamma subdomain of the B-chain results in a significantly, different conformation of the sugar-binding pocket. A ribosome-recognition, site has also been identified in HmRip. The site is a shallow cavity, with, the conserved residues Arg51, Asp70, Thr72 and Asn73 involved in the, binding. The conformations of the antigenic epitopes of residues 1-20, 85-103 and 206-223 differ from those observed in other type II RIPs, resulting in the distinct antigenicity and pharmacological properties of, HmRip.

== Structural highlights ==

<table><tr><td colspan='2'>[[1pc8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Viscum_album Viscum album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PC8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PC8 FirstGlance]. <br>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.8Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pc8 OCA], [https://pdbe.org/1pc8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pc8 RCSB], [https://www.ebi.ac.uk/pdbsum/1pc8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pc8 ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/ML4_VISAL ML4_VISAL] The A chain is responsible for inhibiting protein synthesis through the catalytic inactivation of 60S ribosomal subunits by removing adenine from position 4,324 of 28S rRNA. The B chain binds to cell receptors and probably facilitates the entry into the cell of the A chain; B chains are also responsible for cell agglutination (lectin activity). Inhibits growth of the human tumor cell line Molt4.<ref>PMID:15001393</ref> <ref>PMID:1450445</ref> [UniProtKB:P81446]

== Evolutionary Conservation ==

[[Image:Consurf_key_small.gif|200px|right]]

Check<jmol>

<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pc/1pc8_consurf.spt"</scriptWhenChecked>

<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>

<text>to colour the structure by Evolutionary Conservation</text>

</jmolCheckbox>

</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1pc8 ConSurf].

== Publication Abstract from PubMed ==

This is the first report of the structural studies of a novel ribosome-inactivating protein (RIP) obtained from the Himalayan mistletoe (Viscum album) (HmRip). HmRip is a type II heterodimeric protein consisting of a toxic enzyme (A-chain) with an active site for ribosome inactivation and a lectin subunit (B-chain) with well defined sugar-binding sites. The crystal structure of HmRip has been determined at 3.8 A resolution and refined to a crystallographic R factor of 0.228 (R(free) = 0.271). A comparison of this structure with other type II RIPs reveals the presence of distinct structural features in the active site of the A-chain and in the 2gamma sugar-binding site of the B-chain. The conformation of the side chain of Tyr110, which is a conserved active-site residue in the A subunit, is strikingly different from those observed in other mistletoe RIPs, indicating its unique substrate-binding preference. The deletion of two important residues from the kink region after Ala231 in the 2gamma subdomain of the B-chain results in a significantly different conformation of the sugar-binding pocket. A ribosome-recognition site has also been identified in HmRip. The site is a shallow cavity, with the conserved residues Arg51, Asp70, Thr72 and Asn73 involved in the binding. The conformations of the antigenic epitopes of residues 1-20, 85-103 and 206-223 differ from those observed in other type II RIPs, resulting in the distinct antigenicity and pharmacological properties of HmRip.

~~==About this~~ Structure==

Structure of a novel ribosome-inactivating protein from a hemi-parasitic plant inhabiting the northwestern Himalayas.,Mishra V, Ethayathulla AS, Sharma RS, Yadav S, Krauspenhaar R, Betzel C, Babu CR, Singh TP Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 2):2295-304., Epub 2004 Nov 26. PMID:15583377<ref>PMID:15583377</ref>

~~1PC8 is~~ a ~~[http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences~~ from ~~[http://en~~.~~wikipedia~~.~~org/wiki/Viscum_album Viscum album] with NAG as [http~~:~~//en~~.~~wikipedia.org/wiki/ligand ligand]. Active as [http://en~~.~~wikipedia.org/wiki/rRNA_N-glycosylase rRNA N-glycosylase], with EC number [http~~:~~//www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.22 3.2.2.22] Full crystallographic information is available from [http~~:/~~/ispc.weizmann.ac.il/oca-bin/ocashort?id=1PC8 OCA].~~

~~==Reference==~~

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

~~Structure~~ of ~~a novel ribosome-inactivating protein from a hemi-parasitic plant inhabiting~~ the ~~northwestern Himalayas~~.~~, Mishra V, Ethayathulla AS, Sharma RS, Yadav~~ S~~, Krauspenhaar R, Betzel C, Babu CR, Singh TP, Acta Crystallogr D Biol Crystallogr~~. ~~2004 Dec;60(Pt 12 Pt 2):2295~~-~~304., Epub 2004 Nov 26. PMID~~:[~~http:~~//~~ispc.weizmann.ac.il//pmbin/getpm?pmid=15583377 15583377]~~

</div>

[[Category: ~~Protein complex~~]]

==See Also==

*[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]]

== References ==

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Viscum album]]

~~[[Category: rRNA N-glycosylase]]~~

[[Category: Babu CR]]

[[Category: Babu~~, C.R.~~]]

[[Category: Ethayathulla AS]]

[[Category: Ethayathulla~~, A.S.~~]]

[[Category: Kaur P]]

[[Category: Kaur, P.]]

[[Category: Mishra V]]

[[Category: Mishra, V.]]

[[Category: Paramasivam M]]

[[Category: Paramasivam, M.]]

[[Category: Sharma RS]]

[[Category: Sharma~~, R.S.~~]]

[[Category: Singh G]]

[[Category: Singh, G.]]

[[Category: Singh TP]]

[[Category: Singh~~, T.P.~~]]

[[Category: Yadav S]]

[[Category: Yadav, S.]]

~~[[Category: NAG]]~~

~~[[Category: crystal structure]]~~

~~[[Category: mistletoe lectin]]~~

~~[[Category: novel form]]~~

~~''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 23:40:50 2007''~~

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@@ Line 1: / Line 1: @@
-[[Image:1pc8.gif|left|200px]]<br /><applet load="1pc8" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1pc8, resolution 3.80&Aring;" />
-'''Crystal Structure of a novel form of mistletoe lectin from Himalayan Viscum album L. at 3.8A resolution'''<br />
-==Overview==
+==Crystal Structure of a novel form of mistletoe lectin from Himalayan Viscum album L. at 3.8A resolution==
-This is the first report of the structural studies of a novel, ribosome-inactivating protein (RIP) obtained from the Himalayan mistletoe, (Viscum album) (HmRip). HmRip is a type II heterodimeric protein, consisting of a toxic enzyme (A-chain) with an active site for ribosome, inactivation and a lectin subunit (B-chain) with well defined, sugar-binding sites. The crystal structure of HmRip has been determined at, 3.8 A resolution and refined to a crystallographic R factor of 0.228, (R(free) = 0.271). A comparison of this structure with other type II RIPs, reveals the presence of distinct structural features in the active site of, the A-chain and in the 2gamma sugar-binding site of the B-chain. The, conformation of the side chain of Tyr110, which is a conserved active-site, residue in the A subunit, is strikingly different from those observed in, other mistletoe RIPs, indicating its unique substrate-binding preference., The deletion of two important residues from the kink region after Ala231, in the 2gamma subdomain of the B-chain results in a significantly, different conformation of the sugar-binding pocket. A ribosome-recognition, site has also been identified in HmRip. The site is a shallow cavity, with, the conserved residues Arg51, Asp70, Thr72 and Asn73 involved in the, binding. The conformations of the antigenic epitopes of residues 1-20, 85-103 and 206-223 differ from those observed in other type II RIPs, resulting in the distinct antigenicity and pharmacological properties of, HmRip.
+<StructureSection load='1pc8' size='340' side='right'caption='[[1pc8]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1pc8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Viscum_album Viscum album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PC8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PC8 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pc8 OCA], [https://pdbe.org/1pc8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pc8 RCSB], [https://www.ebi.ac.uk/pdbsum/1pc8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pc8 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ML4_VISAL ML4_VISAL] The A chain is responsible for inhibiting protein synthesis through the catalytic inactivation of 60S ribosomal subunits by removing adenine from position 4,324 of 28S rRNA. The B chain binds to cell receptors and probably facilitates the entry into the cell of the A chain; B chains are also responsible for cell agglutination (lectin activity). Inhibits growth of the human tumor cell line Molt4.<ref>PMID:15001393</ref> <ref>PMID:1450445</ref> [UniProtKB:P81446]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pc/1pc8_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1pc8 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+This is the first report of the structural studies of a novel ribosome-inactivating protein (RIP) obtained from the Himalayan mistletoe (Viscum album) (HmRip). HmRip is a type II heterodimeric protein consisting of a toxic enzyme (A-chain) with an active site for ribosome inactivation and a lectin subunit (B-chain) with well defined sugar-binding sites. The crystal structure of HmRip has been determined at 3.8 A resolution and refined to a crystallographic R factor of 0.228 (R(free) = 0.271). A comparison of this structure with other type II RIPs reveals the presence of distinct structural features in the active site of the A-chain and in the 2gamma sugar-binding site of the B-chain. The conformation of the side chain of Tyr110, which is a conserved active-site residue in the A subunit, is strikingly different from those observed in other mistletoe RIPs, indicating its unique substrate-binding preference. The deletion of two important residues from the kink region after Ala231 in the 2gamma subdomain of the B-chain results in a significantly different conformation of the sugar-binding pocket. A ribosome-recognition site has also been identified in HmRip. The site is a shallow cavity, with the conserved residues Arg51, Asp70, Thr72 and Asn73 involved in the binding. The conformations of the antigenic epitopes of residues 1-20, 85-103 and 206-223 differ from those observed in other type II RIPs, resulting in the distinct antigenicity and pharmacological properties of HmRip.
-==About this Structure==
+Structure of a novel ribosome-inactivating protein from a hemi-parasitic plant inhabiting the northwestern Himalayas.,Mishra V, Ethayathulla AS, Sharma RS, Yadav S, Krauspenhaar R, Betzel C, Babu CR, Singh TP Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 2):2295-304., Epub 2004 Nov 26. PMID:15583377<ref>PMID:15583377</ref>
-PC8 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Viscum_album Viscum album] with NAG as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/rRNA_N-glycosylase rRNA N-glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.22 3.2.2.22] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1PC8 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structure of a novel ribosome-inactivating protein from a hemi-parasitic plant inhabiting the northwestern Himalayas., Mishra V, Ethayathulla AS, Sharma RS, Yadav S, Krauspenhaar R, Betzel C, Babu CR, Singh TP, Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 2):2295-304., Epub 2004 Nov 26. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15583377 15583377]
+</div>
-[[Category: Protein complex]]
+<div class="pdbe-citations 1pc8" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Viscum album]]
-[[Category: rRNA N-glycosylase]]
+[[Category: Babu CR]]
-[[Category: Babu, C.R.]]
+[[Category: Ethayathulla AS]]
-[[Category: Ethayathulla, A.S.]]
+[[Category: Kaur P]]
-[[Category: Kaur, P.]]
+[[Category: Mishra V]]
-[[Category: Mishra, V.]]
+[[Category: Paramasivam M]]
-[[Category: Paramasivam, M.]]
+[[Category: Sharma RS]]
-[[Category: Sharma, R.S.]]
+[[Category: Singh G]]
-[[Category: Singh, G.]]
+[[Category: Singh TP]]
-[[Category: Singh, T.P.]]
+[[Category: Yadav S]]
-[[Category: Yadav, S.]]
-[[Category: NAG]]
-[[Category: crystal structure]]
-[[Category: mistletoe lectin]]
-[[Category: novel form]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 23:40:50 2007''