This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1yf8

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 16:43, 29 January 2020

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

Structural highlights

1yf8 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.
Ligands:	, , , , ,
Activity:	rRNA N-glycosylase, with EC number 3.2.2.22
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

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.

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^[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, Bilgrami S, Sharma RS, Kaur P, Yadav S, Krauspenhaar R, Betzel C, Voelter W, Babu CR, Singh TP. Crystal structure of himalayan mistletoe ribosome-inactivating protein reveals the presence of a natural inhibitor and a new functionally active sugar-binding site. J Biol Chem. 2005 May 27;280(21):20712-21. Epub 2005 Mar 17. PMID:15774467 doi:10.1074/jbc.M500735200

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/1yf8"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Himalayan mistletoe RIP reveals the presence of a natural inhibitor and a new functionally active sugar-binding site==
-<StructureSection load='1yf8' size='340' side='right' caption='[[1yf8]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+<StructureSection load='1yf8' size='340' side='right'caption='[[1yf8]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
 <table><tr><td colspan='2'>[[1yf8]] 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=1YF8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YF8 FirstGlance]. <br>
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Viscum album]]
 [[Category: RRNA N-glycosylase]]

1yf8

From Proteopedia

Revision as of 16:43, 29 January 2020

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox