1kd1: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1kd1.gif|left|200px]]
- {{Structure
+==Co-crystal Structure of Spiramycin bound to the 50S Ribosomal Subunit of Haloarcula marismortui==
-|PDB= 1kd1 |SIZE=350|CAPTION= <scene name='initialview01'>1kd1</scene>, resolution 3.00&Aring;
+<StructureSection load='1kd1' size='340' side='right'caption='[[1kd1]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SPR:SPIRAMYCIN+I'>SPR</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
+<table><tr><td colspan='2'>[[1kd1]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KD1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KD1 FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SPR:SPIRAMYCIN+I'>SPR</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kd1 OCA], [https://pdbe.org/1kd1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kd1 RCSB], [https://www.ebi.ac.uk/pdbsum/1kd1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kd1 ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1k73|1K73]], [[1k8a|1K8A]], [[1k9m|1K9M]], [[1kc8|1KC8]], [[1m1k|1M1K]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kd1 OCA], [http://www.ebi.ac.uk/pdbsum/1kd1 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1kd1 RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/RL2_HALMA RL2_HALMA] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01320_A]
+== 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/kd/1kd1_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/main_output.php?pdb_ID=1kd1 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Crystal structures of the Haloarcula marismortui large ribosomal subunit complexed with the 16-membered macrolide antibiotics carbomycin A, spiramycin, and tylosin and a 15-membered macrolide, azithromycin, show that they bind in the polypeptide exit tunnel adjacent to the peptidyl transferase center. Their location suggests that they inhibit protein synthesis by blocking the egress of nascent polypeptides. The saccharide branch attached to C5 of the lactone rings extends toward the peptidyl transferase center, and the isobutyrate extension of the carbomycin A disaccharide overlaps the A-site. Unexpectedly, a reversible covalent bond forms between the ethylaldehyde substituent at the C6 position of the 16-membered macrolides and the N6 of A2103 (A2062, E. coli). Mutations in 23S rRNA that result in clinical resistance render the binding site less complementary to macrolides.
-'''Co-crystal Structure of Spiramycin bound to the 50S Ribosomal Subunit of Haloarcula marismortui'''
+The structures of four macrolide antibiotics bound to the large ribosomal subunit.,Hansen JL, Ippolito JA, Ban N, Nissen P, Moore PB, Steitz TA Mol Cell. 2002 Jul;10(1):117-28. PMID:12150912<ref>PMID:12150912</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1kd1" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Crystal structures of the Haloarcula marismortui large ribosomal subunit complexed with the 16-membered macrolide antibiotics carbomycin A, spiramycin, and tylosin and a 15-membered macrolide, azithromycin, show that they bind in the polypeptide exit tunnel adjacent to the peptidyl transferase center. Their location suggests that they inhibit protein synthesis by blocking the egress of nascent polypeptides. The saccharide branch attached to C5 of the lactone rings extends toward the peptidyl transferase center, and the isobutyrate extension of the carbomycin A disaccharide overlaps the A-site. Unexpectedly, a reversible covalent bond forms between the ethylaldehyde substituent at the C6 position of the 16-membered macrolides and the N6 of A2103 (A2062, E. coli). Mutations in 23S rRNA that result in clinical resistance render the binding site less complementary to macrolides.
+*[[Ribosome 3D structures|Ribosome 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-KD1 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KD1 OCA].
+__TOC__
+</StructureSection>
-==Reference==
-The structures of four macrolide antibiotics bound to the large ribosomal subunit., Hansen JL, Ippolito JA, Ban N, Nissen P, Moore PB, Steitz TA, Mol Cell. 2002 Jul;10(1):117-28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12150912 12150912]
 [[Category: Haloarcula marismortui]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Ban, N.]]
+[[Category: Ban N]]
-[[Category: Hansen, J L.]]
+[[Category: Hansen JL]]
-[[Category: Ippolito, J A.]]
+[[Category: Ippolito JA]]
-[[Category: Moore, P B.]]
+[[Category: Moore PB]]
-[[Category: Nissen, P.]]
+[[Category: Nissen P]]
-[[Category: Steitz, T A.]]
+[[Category: Steitz TA]]
-[[Category: 50s subunit]]
-[[Category: antibiotic]]
-[[Category: carbinolamine]]
-[[Category: macrolide]]
-[[Category: spiramycin]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:46:44 2008''