1l4h: Difference between revisions

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-{{Seed}}
-[[Image:1l4h.png|left|200px]]
-<!--
+==Crystal Structure of CobT complexed with indole and nicotinate mononucleotide==
-The line below this paragraph, containing "STRUCTURE_1l4h", creates the "Structure Box" on the page.
+<StructureSection load='1l4h' size='340' side='right'caption='[[1l4h]], [[Resolution|resolution]] 2.10&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'>[[1l4h]] 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=1L4H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L4H 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]] 2.1&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IND:INDOLE'>IND</scene>, <scene name='pdbligand=NCN:NICOTINATE+MONONUCLEOTIDE'>NCN</scene></td></tr>
-{{STRUCTURE_1l4h|  PDB=1l4h  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1l4h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l4h OCA], [https://pdbe.org/1l4h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l4h RCSB], [https://www.ebi.ac.uk/pdbsum/1l4h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l4h 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/l4/1l4h_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1l4h 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.
-===Crystal Structure of CobT complexed with indole and nicotinate mononucleotide===
+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 1l4h" 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]]
-L4H is a 1 chain 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=1L4H OCA].
-==Reference==
-<ref group="xtra">PMID:12119022</ref><references group="xtra"/>
-[[Category: Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase]]
 [[Category: Salmonella enterica]]
-[[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 Feb 18 02:52:11 2009''