1yf8

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[[Image:1yf8.gif|left|200px]]<br /><applet load="1yf8" size="350" color="white" frame="true" align="right" spinBox="true"
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[[Image:1yf8.gif|left|200px]]
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caption="1yf8, resolution 2.80&Aring;" />
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'''Crystal structure of Himalayan mistletoe RIP reveals the presence of a natural inhibitor and a new functionally active sugar-binding site'''<br />
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{{Structure
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|PDB= 1yf8 |SIZE=350|CAPTION= <scene name='initialview01'>1yf8</scene>, resolution 2.80&Aring;
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|SITE=
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|LIGAND= <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene> and <scene name='pdbligand=P6C:2-AMINO-4-ISOPROPYL-PTERIDINE-6-CARBOXYLIC ACID'>P6C</scene>
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|ACTIVITY= [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]
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|GENE=
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}}
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'''Crystal structure of Himalayan mistletoe RIP reveals the presence of a natural inhibitor and a new functionally active sugar-binding site'''
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==Overview==
==Overview==
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==About this Structure==
==About this Structure==
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1YF8 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 <scene name='pdbligand=NAG:'>NAG</scene>, <scene name='pdbligand=GAL:'>GAL</scene> and <scene name='pdbligand=P6C:'>P6C</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1YF8 OCA].
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1YF8 is a [[Protein complex]] structure of sequences 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=1YF8 OCA].
==Reference==
==Reference==
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Crystal structure of himalayan mistletoe ribosome-inactivating protein reveals the presence of a natural inhibitor and a new functionally active sugar-binding site., Mishra V, Bilgrami S, Sharma RS, Kaur P, Yadav S, Krauspenhaar R, Betzel C, Voelter W, Babu CR, Singh TP, J Biol Chem. 2005 May 27;280(21):20712-21. Epub 2005 Mar 17. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15774467 15774467]
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Crystal structure of himalayan mistletoe ribosome-inactivating protein reveals the presence of a natural inhibitor and a new functionally active sugar-binding site., Mishra V, Bilgrami S, Sharma RS, Kaur P, Yadav S, Krauspenhaar R, Betzel C, Voelter W, Babu CR, Singh TP, J Biol Chem. 2005 May 27;280(21):20712-21. Epub 2005 Mar 17. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15774467 15774467]
[[Category: Protein complex]]
[[Category: Protein complex]]
[[Category: Viscum album]]
[[Category: Viscum album]]
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[[Category: viscum album]]
[[Category: viscum album]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:04:49 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:22:05 2008''

Revision as of 13:22, 20 March 2008

Image:1yf8.gif


PDB ID 1yf8

Drag the structure with the mouse to rotate
, resolution 2.80Å
Ligands: , and
Activity: rRNA N-glycosylase, with EC number 3.2.2.22
Coordinates: save as pdb, mmCIF, xml



Crystal structure of Himalayan mistletoe RIP reveals the presence of a natural inhibitor and a new functionally active sugar-binding site


Overview

Ribosome-inactivating proteins (RIPs) are toxins involved in plant defense. How the plant prevents autotoxicity is not yet fully understood. The present study is the first structural evidence of a naturally inhibited form of RIP from a plant. Himalayan mistletoe RIP (HmRIP) was purified from Viscum album leaves and crystallized with lactose. The structure was determined by the molecular replacement method and refined at 2.8-A resolution. The crystal structure revealed the presence of high quality non-protein electron density at the active site, into which a pteridine derivative (2-amino 4-isopropyl 6-carboxyl pteridine) was modeled. The carboxyl group of the ligand binds strongly with the key active site residue Arg(162), nullifies the positive charge required for catalysis, and thereby acts as a natural inhibitor. Lectin subunits of RIPs have two active sugar-binding sites present in 1alpha- and 2gamma-subdomains. A third functionally active site has been identified in the 1beta-subdomain of HmRIP. The 1beta-site is active despite the absence of conserved polar sugar-binding residues. Loss of these residues is compensated by the following: (i) the presence of an extended site where the penultimate sugar also interacts with the protein; (ii) the interactions of galactose with the protein main chain carbonyl and amide nitrogen atoms; (iii) the presence of a well defined pocket encircled by four walls; and (iv) a favorable stacking of the galactose ring with Tyr(66) besides the conserved Phe(75). The mode of sugar binding is also distinct at the 1alpha and 2gamma sugar-binding sites.

About this Structure

1YF8 is a Protein complex structure of sequences from Viscum album. Full crystallographic information is available from OCA.

Reference

Crystal structure of himalayan mistletoe ribosome-inactivating protein reveals the presence of a natural inhibitor and a new functionally active sugar-binding site., Mishra V, Bilgrami S, Sharma RS, Kaur P, Yadav S, Krauspenhaar R, Betzel C, Voelter W, Babu CR, Singh TP, J Biol Chem. 2005 May 27;280(21):20712-21. Epub 2005 Mar 17. PMID:15774467

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