3mdf

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the RRM domain of Cyclophilin 33

Structural highlights

3mdf is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.85Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PPIE_HUMAN PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. Combines RNA-binding and PPIase activities. May be involved in muscle- and brain-specific processes. May be involved in pre-mRNA splicing.

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

The nuclear protein cyclophilin 33 (Cyp33) is a peptidyl-prolyl cis-trans isomerase that catalyzes cis-trans isomerization of the peptide bond preceding a proline and promotes folding and conformational changes in folded and unfolded proteins. The N-terminal RNA-recognition motif (RRM) domain of Cyp33 has been found to associate with the third plant homeodomain (PHD3) finger of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly(A) RNA sequence. Here, we report a 1.9 A resolution crystal structure of the RRM domain of Cyp33 and describe the molecular mechanism of PHD3 and RNA recognition. The Cyp33 RRM domain folds into a five-stranded antiparallel beta-sheet and two alpha-helices. The RRM domain, but not the catalytic module of Cyp33, binds strongly to PHD3, exhibiting a 2 muM affinity as measured by isothermal titration calorimetry. NMR chemical shift perturbation (CSP) analysis and dynamics data reveal that the beta strands and the beta2-beta3 loop of the RRM domain are involved in the interaction with PHD3. Mutations in the PHD3-binding site or deletions in the beta2-beta3 loop lead to a significantly reduced affinity or abrogation of the interaction. The RNA-binding pocket of the Cyp33 RRM domain, mapped on the basis of NMR CSP and mutagenesis, partially overlaps with the PHD3-binding site, and RNA association is abolished in the presence of MLL PHD3. Full-length Cyp33 acts as a negative regulator of MLL-induced transcription and reduces the expression levels of MLL target genes MEIS1 and HOXA9. Together, these in vitro and in vivo data provide insight into the multiple functions of Cyp33 RRM and suggest a Cyp33-dependent mechanism for regulating the transcriptional activity of MLL.

Molecular mechanism of MLL PHD3 and RNA recognition by the Cyp33 RRM domain.,Hom RA, Chang PY, Roy S, Musselman CA, Glass KC, Selezneva AI, Gozani O, Ismagilov RF, Cleary ML, Kutateladze TG J Mol Biol. 2010 Jul 9;400(2):145-54. Epub 2010 May 8. PMID:20460131^[1]

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

References

↑ Hom RA, Chang PY, Roy S, Musselman CA, Glass KC, Selezneva AI, Gozani O, Ismagilov RF, Cleary ML, Kutateladze TG. Molecular mechanism of MLL PHD3 and RNA recognition by the Cyp33 RRM domain. J Mol Biol. 2010 Jul 9;400(2):145-54. Epub 2010 May 8. PMID:20460131 doi:10.1016/j.jmb.2010.04.067

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/3mdf"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the RRM domain of Cyclophilin 33==
-<StructureSection load='3mdf' size='340' side='right' caption='[[3mdf]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+<StructureSection load='3mdf' size='340' side='right'caption='[[3mdf]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3mdf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MDF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3MDF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3mdf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MDF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MDF FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PPIE, CYP33 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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]] 1.85&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </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=3mdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mdf OCA], [https://pdbe.org/3mdf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3mdf RCSB], [https://www.ebi.ac.uk/pdbsum/3mdf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3mdf 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=3mdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mdf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3mdf RCSB], [http://www.ebi.ac.uk/pdbsum/3mdf PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PPIE_HUMAN PPIE_HUMAN]] PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. Combines RNA-binding and PPIase activities. May be involved in muscle- and brain-specific processes. May be involved in pre-mRNA splicing.
+[https://www.uniprot.org/uniprot/PPIE_HUMAN PPIE_HUMAN] PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. Combines RNA-binding and PPIase activities. May be involved in muscle- and brain-specific processes. May be involved in pre-mRNA splicing.
 == 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/md/3mdf_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/md/3mdf_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=3mdf ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3mdf" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Cyclophilin|Cyclophilin]]
+*[[Cyclophilin 3D structures|Cyclophilin 3D structures]]
 == References ==
 <references/>
@@ Line 35: / Line 36: @@
 </StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Peptidylprolyl isomerase]]
+[[Category: Large Structures]]
-[[Category: Chang, P Y]]
+[[Category: Chang PY]]
-[[Category: Cleary, M L]]
+[[Category: Cleary ML]]
-[[Category: Glass, K C]]
+[[Category: Glass KC]]
-[[Category: Gozani, O]]
+[[Category: Gozani O]]
-[[Category: Hom, R A]]
+[[Category: Hom RA]]
-[[Category: Ismagilov, R F]]
+[[Category: Ismagilov RF]]
-[[Category: Kutateladze, T G]]
+[[Category: Kutateladze TG]]
-[[Category: Mussleman, C A]]
+[[Category: Mussleman CA]]
-[[Category: Roy, S]]
+[[Category: Roy S]]
-[[Category: Seleznevia, A I]]
+[[Category: Seleznevia AI]]
-[[Category: Cyp33]]
-[[Category: Isomerase]]
-[[Category: Mll]]
-[[Category: Mrna processing]]
-[[Category: Mrna splicing]]
-[[Category: Nucleus]]
-[[Category: Phd finger]]
-[[Category: Rna binding protein]]
-[[Category: Rna-binding]]
-[[Category: Rotamase]]
-[[Category: Rrm domain]]
-[[Category: Spliceosome]]

3mdf

From Proteopedia

Current revision

Crystal structure of the RRM domain of Cyclophilin 33

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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