1l4e: Difference between revisions

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-{{Seed}}
-[[Image:1l4e.png|left|200px]]
-<!--
+==The crystal structure of CobT complexed with alpha-ribazole-5'-phosphate==
-The line below this paragraph, containing "STRUCTURE_1l4e", creates the "Structure Box" on the page.
+<StructureSection load='1l4e' size='340' side='right'caption='[[1l4e]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1l4e]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica Salmonella enterica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L4E FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=RBZ:ALPHA-RIBAZOLE-5-PHOSPHATE'>RBZ</scene></td></tr>
-{{STRUCTURE_1l4e|  PDB=1l4e  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1l4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l4e OCA], [https://pdbe.org/1l4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l4e RCSB], [https://www.ebi.ac.uk/pdbsum/1l4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l4e ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/COBT_SALTY COBT_SALTY] Catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide (NAMN) and 5,6-dimethylbenzimidazole (DMB).
+== 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/l4/1l4e_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=1l4e ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Nicotinate mononucleotide (NaMN):5,6-dimethylbenzimidazole (DMB) phosphoribosyltransferase (CobT) from Salmonella enterica plays a central role in the synthesis of alpha-ribazole-5'-phosphate, an intermediate for the lower ligand of cobalamin. In earlier studies it proved difficult to obtain the structure of CobT bound to NaMN because it is hydrolyzed in the crystal lattice in the absence of the second substrate DMB. In an effort to map the reaction pathway of this enzyme, NaMN was captured in the active site with the substrate analogs 4,5-dimethyl-1,2-phenylenediamine, 4-methylcatechol, indole, 3,4-dimethylaniline, 2,5-dimethylaniline, 3,4-dimethylphenol, and 2-amino-p-cresol. Structures of these complexes reveal that they exclude water molecules responsible for the hydrolysis from the active site. These structures, together with the early complexes with alpha-ribazole-5'-phosphate and DMB, provide a complete description of the reaction pathway. They demonstrate that the nicotinate moiety and phosphate do not appear to move significantly between reactants and products but that the aromatic base and ribose moiety each move approximately 1.2 A toward each other in the transformation. This study also reveals that, like many other nucleotide binding proteins, coordination of DMB is accompanied by a disorder-order transition in a surface loop. The structure of apo-CobT is also reported.
-===The crystal structure of CobT complexed with alpha-ribazole-5'-phosphate===
+Capture of a labile substrate by expulsion of water molecules from the active site of nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) from Salmonella enterica.,Cheong CG, Escalante-Semerena JC, Rayment I J Biol Chem. 2002 Oct 25;277(43):41120-7. Epub 2002 Jul 5. PMID:12101181<ref>PMID:12101181</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1l4e" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12119022}}, adds the Publication Abstract to the page
+*[[Phosphoribosyltransferase 3D structures|Phosphoribosyltransferase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12119022 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12119022}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-L4E is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica Salmonella enterica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L4E OCA].
-==Reference==
-Structural studies of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica: the apo, substrate, and product-aldimine complexes., Cheong CG, Escalante-Semerena JC, Rayment I, Biochemistry. 2002 Jul 23;41(29):9079-89. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12119022 12119022]
-[[Category: Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase]]
 [[Category: Salmonella enterica]]
-[[Category: Single protein]]
+[[Category: Cheong C-G]]
-[[Category: Cheong, C G.]]
+[[Category: Escalante-Semerena J]]
-[[Category: Escalante-Semerena, J.]]
+[[Category: Rayment I]]
-[[Category: Rayment, I.]]
-[[Category: 5,6-dimethylbenzimidazole]]
-[[Category: Cobalamin synthetic enzyme]]
-[[Category: Cobt]]
-[[Category: Nicotinate mononucleotide]]
-[[Category: Phosphoribosyltransferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul  2 11:41:03 2008''