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1pc8

From Proteopedia

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

Structural highlights

1pc8 is a 2 chain structure with sequence from Viscum album. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.8Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1] ^[2] [UniProtKB:P81446]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from 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.

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^[3]

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

References

↑ Mishra V, Sharma RS, Yadav S, Babu CR, Singh TP. Purification and characterization of four isoforms of Himalayan mistletoe ribosome-inactivating protein from Viscum album having unique sugar affinity. Arch Biochem Biophys. 2004 Mar 15;423(2):288-301. PMID:15001393 doi:http://dx.doi.org/10.1016/j.abb.2003.12.033
↑ Dietrich JB, Ribereau-Gayon G, Jung ML, Franz H, Beck JP, Anton R. Identity of the N-terminal sequences of the three A chains of mistletoe (Viscum album L.) lectins: homology with ricin-like plant toxins and single-chain ribosome-inhibiting proteins. Anticancer Drugs. 1992 Oct;3(5):507-11. PMID:1450445
↑ Mishra V, Ethayathulla AS, Sharma RS, Yadav S, Krauspenhaar R, Betzel C, Babu CR, Singh TP. Structure of a novel ribosome-inactivating protein from a hemi-parasitic plant inhabiting the northwestern Himalayas. Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 2):2295-304., Epub 2004 Nov 26. PMID:15583377 doi:10.1107/S0907444904023534

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1pc8"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of a novel form of mistletoe lectin from Himalayan Viscum album L. at 3.8A resolution==
-<StructureSection load='1pc8' size='340' side='right' caption='[[1pc8]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
+<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 [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PC8 FirstGlance]. <br>
+<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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene></td></tr>
+</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1mqc|1mqc]]</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></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>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1pc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pc8 OCA], [http://pdbe.org/1pc8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pc8 RCSB], [http://www.ebi.ac.uk/pdbsum/1pc8 PDBsum]</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>
+    <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/initialview01.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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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;">
@@ Line 31: / Line 33: @@
 __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: Hydrolase]]
-[[Category: Mistletoe lectin]]
-[[Category: Novel form]]

1pc8

From Proteopedia

Current revision

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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