4ii2: Difference between revisions

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 ==Crystal structure of Ubiquitin activating enzyme 1 (Uba1) in complex with the Ub E2 Ubc4, ubiquitin, and ATP/Mg==
-<StructureSection load='4ii2' size='340' side='right' caption='[[4ii2]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+<StructureSection load='4ii2' size='340' side='right'caption='[[4ii2]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4ii2]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Fission_yeast Fission yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4II2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4II2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4ii2]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe_972h- Schizosaccharomyces pombe 972h-]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4II2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4II2 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PG0:2-(2-METHOXYETHOXY)ETHANOL'>PG0</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ii3|4ii3]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PG0:2-(2-METHOXYETHOXY)ETHANOL'>PG0</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ptr3, SPBC1604.21c, SPBC211.09, Ubiquitin activating enzyme 1 (Uba1) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast]), ubi2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast]), SPBC119.02, ubc4, Ubiquitin conjugating enzyme 4 (Ubc4) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast])</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=4ii2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ii2 OCA], [https://pdbe.org/4ii2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ii2 RCSB], [https://www.ebi.ac.uk/pdbsum/4ii2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ii2 ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquitin--protein_ligase Ubiquitin--protein ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.19 6.3.2.19] </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=4ii2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ii2 OCA], [http://pdbe.org/4ii2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ii2 RCSB], [http://www.ebi.ac.uk/pdbsum/4ii2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ii2 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/UBA1_SCHPO UBA1_SCHPO]] Activates ubiquitin by first adenylating its C-terminal glycine residue with ATP, and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding an ubiquitin-E1 thioester and free AMP. [[http://www.uniprot.org/uniprot/UBC4_SCHPO UBC4_SCHPO]] Catalyzes the covalent attachment of ubiquitin to other proteins. Mediates the selective degradation of short-lived and abnormal proteins. Mediates ubiquitination of PEX5 (By similarity). [[http://www.uniprot.org/uniprot/RL402_SCHPO RL402_SCHPO]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, and DNA-damage responses. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling (By similarity).  Ribosomal protein L40 is a component of the 60S subunit of the ribosome.
+[https://www.uniprot.org/uniprot/UBA1_SCHPO UBA1_SCHPO] Activates ubiquitin by first adenylating its C-terminal glycine residue with ATP, and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding an ubiquitin-E1 thioester and free AMP.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 19: @@
 </div>
 <div class="pdbe-citations 4ii2" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ribosomal protein L40|Ribosomal protein L40]]
+*[[3D structures of Ubiquitin activating enzyme|3D structures of Ubiquitin activating enzyme]]
+*[[3D structures of ubiquitin conjugating enzyme|3D structures of ubiquitin conjugating enzyme]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Fission yeast]]
+[[Category: Large Structures]]
-[[Category: Ubiquitin--protein ligase]]
+[[Category: Schizosaccharomyces pombe 972h-]]
-[[Category: Lima, C D]]
+[[Category: Lima CD]]
-[[Category: Olsen, S K]]
+[[Category: Olsen SK]]
-[[Category: Adenylation]]
-[[Category: Atp-binding]]
-[[Category: Atp/mg binding]]
-[[Category: Conformational change]]
-[[Category: E1]]
-[[Category: E2]]
-[[Category: Ligase]]
-[[Category: Ligase activity]]
-[[Category: Nucleus]]
-[[Category: Rossmann-like fold]]
-[[Category: Thioester]]
-[[Category: Uba1]]
-[[Category: Ubc4]]
-[[Category: Ubiquitin]]
-[[Category: Ubiquitin e2 binding]]
-[[Category: Ubiquitin-like fold]]
-[[Category: Ubiquitination]]