1cf5

From Proteopedia

(Difference between revisions)

Current revision

BETA-MOMORCHARIN STRUCTURE AT 2.55 A

Structural highlights

1cf5 is a 2 chain structure with sequence from Momordica charantia. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.55Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RIP3_MOMCH Irreversibly relaxes supercoiled DNA and catalyzes double-stranded breakage. Acts also as a ribosome inactivating protein.

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

Beta-Momorcharin (Mr approximately 29 kDa) is a single-chained ribosome-inactivating protein (RIP) with a branched hexasaccharide bound to Asn51. The crystal structure of beta-momorcharin has been determined using the molecular-replacement method and refined to 2. 55 A resolution. The final structural model gave an R factor of 17. 2% and root-mean-square deviations of 0.016 A and 1.76 degrees from ideal bond lengths and bond angles, respectively. beta-Momorcharin contains nine alpha-helices, two 310 helices and three beta-sheets, and its overall structure is similar to those of other single-chained RIPs. Residues Tyr70, Tyr109, Glu158 and Arg161 are expected to define the active site of beta-momorcharin as an rRNA N-glycosidase. The oligosaccharide is linked to the protein through an N-glycosidic bond, beta-GlcNAc-(1-N)-Asn51, and stretches from the surface of the N-terminal domain far from the active site, which suggests that it should not play a role in enzymatic function. The oligosaccharide of each beta-momorcharin molecule interacts with the protein through hydrogen bonds, although in the crystals most of these are intermolecular interactions with the protein atoms in an adjacent unit cell. This is the first example of an RIP structure which provides information about the three-dimensional structure and binding site of the oligosaccharide in the active chains of RIPs.

Three-dimensional structure of beta-momorcharin at 2.55 A resolution.,Yuan YR, He YN, Xiong JP, Xia ZX Acta Crystallogr D Biol Crystallogr. 1999 Jun;55(Pt 6):1144-51. PMID:10329776^[1]

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

References

↑ Yuan YR, He YN, Xiong JP, Xia ZX. Three-dimensional structure of beta-momorcharin at 2.55 A resolution. Acta Crystallogr D Biol Crystallogr. 1999 Jun;55(Pt 6):1144-51. PMID:10329776

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1cf5"

@@ Line 3: / Line 3: @@
 <StructureSection load='1cf5' size='340' side='right'caption='[[1cf5]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1cf5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Momordica_charantia Momordica charantia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CF5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CF5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1cf5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Momordica_charantia Momordica charantia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CF5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CF5 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=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</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]] 2.55&#8491;</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=1cf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cf5 OCA], [http://pdbe.org/1cf5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1cf5 RCSB], [http://www.ebi.ac.uk/pdbsum/1cf5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1cf5 ProSAT]</span></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=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</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=1cf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cf5 OCA], [https://pdbe.org/1cf5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cf5 RCSB], [https://www.ebi.ac.uk/pdbsum/1cf5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cf5 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/RIP3_MOMCH RIP3_MOMCH] Irreversibly relaxes supercoiled DNA and catalyzes double-stranded breakage. Acts also as a ribosome inactivating protein.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 12: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cf/1cf5_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 28: / Line 31: @@
 ==See Also==
-*[[Ribosome inactivating protein|Ribosome inactivating protein]]
+*[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]]
 == References ==
 <references/>
@@ Line 35: / Line 38: @@
 [[Category: Large Structures]]
 [[Category: Momordica charantia]]
-[[Category: He, Y N]]
+[[Category: He Y-N]]
-[[Category: Xia, Z X]]
+[[Category: Xia Z-X]]
-[[Category: Xiong, J P]]
+[[Category: Xiong J-P]]
-[[Category: Yuan, Y R]]
+[[Category: Yuan Y-R]]
-[[Category: Glycoprotein]]
-[[Category: Ribosome-inactivating protein]]
-[[Category: Rna n-glycosidase activity]]

1cf5

From Proteopedia

Current revision

BETA-MOMORCHARIN STRUCTURE AT 2.55 A

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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